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Opened 5 years ago
Last modified 5 years ago
#3950 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
Dear ChimeraX-Team,
I've closed the respective pdb and subsequent saving gives me following error message:
ValueError: error processing: 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z SES surface': Error while saving session data for 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z SES surface'
Is this because of the Intel graphics problem? Can I circumvent this somehow without leaving the pdb(s) open?
Thanks for your help!
Best,
Claudia
Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure4_ArfB.cxs" format session
Log from Fri Nov 13 02:10:38 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure3_ArfA-BrfA.cxs" format session
Log from Fri Nov 13 01:13:06 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure3_ArfA-BrfA.cxs" format session
Log from Thu Nov 12 16:47:41 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure3_ArfA-BrfA.cxs" format session
Frozen name "4v8q_30S" not restored: nothing is selected by specifier
Log from Wed Nov 11 01:27:39 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure3_ArfA-BrfA.cxs" format session
registering illegal selector name "4v8q_30S"
Log from Tue Nov 10 00:04:42 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
registering illegal selector name "4v8q_30S"
Log from Fri Nov 6 22:29:56 2020UCSF ChimeraX version: 1.2.dev202011040611
(2020-11-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure1_Trans-Transl_v2.cxs" format
> session
registering illegal selector name "4v8q_30S"
Log from Tue Nov 3 01:00:53 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure1_Trans-Transl_v2.cxs" format
> session
registering illegal selector name "4v8q_30S"
Log from Mon Nov 2 20:45:29 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure1_Trans-Transl.cxs" format
> session
registering illegal selector name "4v8q_30S"
Log from Sat Oct 31 00:45:10 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\claud\Documents\Reviews\FrontiersReview-Translation
> regulation\Figures\CimeraSessions\ChmX_Figure1_Trans-Transl.cxs" format
> session
registering illegal selector name "4v8q_30S"
Log from Thu Oct 29 23:19:02 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
registering illegal selector name "4v8q_30S"
Log from Thu Oct 29 18:44:58 2020 Startup Messages
---
warning | Your computer has Intel graphics driver 7870 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/claud/Downloads/4v8q-pdb-bundle.tar/4v8q-pdb-
> bundle/4v8q_withEF-Tu.pdb
Summary of feedback from opening C:/Users/claud/Downloads/4v8q-pdb-
bundle.tar/4v8q-pdb-bundle/4v8q_withEF-Tu.pdb
---
warning | Ignored bad PDB record found on line 155403
END
Chain information for 4v8q_withEF-Tu.pdb #1
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> open C:/Users/claud/Downloads/6q97-pdb-bundle.tar/6q97_A-site.pdb
Summary of feedback from opening C:/Users/claud/Downloads/6q97-pdb-
bundle.tar/6q97_A-site.pdb
---
warning | Ignored bad PDB record found on line 157976
END
Chain information for 6q97_A-site.pdb #2
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> open C:/Users/claud/Downloads/4v6t-pdb-bundle.tar/4v6t_withEF-G.pdb
Summary of feedback from opening C:/Users/claud/Downloads/4v6t-pdb-
bundle.tar/4v6t_withEF-G.pdb
---
warning | Ignored bad PDB record found on line 158154
END
Chain information for 4v6t_withEF-G.pdb #3
---
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z | No description available
> open C:/Users/claud/Downloads/6q98-pdb-bundle.tar/6q98_P-site.pdb
Summary of feedback from opening C:/Users/claud/Downloads/6q98-pdb-
bundle.tar/6q98_P-site.pdb
---
warning | Ignored bad PDB record found on line 155175
END
Chain information for 6q98_P-site.pdb #4
---
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> open C:/Users/claud/Downloads/6q9a-pdb-bundle.tar/6q9a_PastP-site.pdb
Summary of feedback from opening C:/Users/claud/Downloads/6q9a-pdb-
bundle.tar/6q9a_PastP-site.pdb
---
warning | Ignored bad PDB record found on line 156504
END
Chain information for 6q9a_PastP-site.pdb #5
---
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> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show cartoons
> hide atoms
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> lighting simple
> set bgColor white
> set bgColor black
> set bgColor gray
> set bgColor black
> preset cartoons/nucleotides ribbons/slabs
Changed 775741 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #5 models
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
62479 atoms, 69979 bonds, 2901 residues, 1 model selected
> select clear
> lighting flat
> lighting flat
> lighting simple
> nucleotides #!1 fill
> style nucleic & #!1 stick
Changed 102049 atom styles
> show #!1 atoms
> hide #!1 atoms
> select up
1530 atoms, 1680 bonds, 89 residues, 1 model selected
> select up
5504 atoms, 5732 bonds, 587 residues, 1 model selected
> select up
154205 atoms, 167270 bonds, 11420 residues, 1 model selected
> select up
777380 atoms, 843073 bonds, 57530 residues, 5 models selected
> select down
154205 atoms, 167270 bonds, 11420 residues, 1 model selected
> select clear
> select up
70163 atoms, 78192 bonds, 3547 residues, 1 model selected
> select up
92785 atoms, 101216 bonds, 6521 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark gray
> color sel light gray
> color sel dark gray
> color sel gray
> color sel dark gray
> select clear
> select #1/4:44
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1640 atoms, 1832 bonds, 77 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> select clear
> select #1/D:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
600 atoms, 606 bonds, 72 residues, 1 model selected
> select up
2375 atoms, 2412 bonds, 291 residues, 1 model selected
> color sel dark gray
> select clear
> select up
1640 atoms, 1832 bonds, 77 residues, 1 model selected
> color sel forest green
> select clear
> select #1/7:197
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
123 atoms, 126 bonds, 14 residues, 1 model selected
> select up
3015 atoms, 3075 bonds, 381 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select clear
> select #1/6:22
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1305 atoms, 1454 bonds, 62 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
> select up
112 atoms, 112 bonds, 13 residues, 1 model selected
> select up
1184 atoms, 1203 bonds, 144 residues, 1 model selected
> ui tool show "Color Actions"
> color sel fire brick
> select clear
> select #1/i:162
22 atoms, 24 bonds, 1 residue, 1 model selected
Drag select of 218 residues
> select clear
> select up
34442 atoms, 38310 bonds, 1764 residues, 1 model selected
> select up
49162 atoms, 53289 bonds, 3600 residues, 1 model selected
> select down
34442 atoms, 38310 bonds, 1764 residues, 1 model selected
> select down
181 atoms, 21 residues, 1 model selected
> select up
34442 atoms, 38310 bonds, 1764 residues, 1 model selected
> select up
49162 atoms, 53289 bonds, 3600 residues, 1 model selected
> name frozen 4v8q_30S sel
registering illegal selector name "4v8q_30S"
> ui tool show "Color Actions"
> color sel light yellow
> color sel lemon chiffon
> color sel lemon chiffon
> color sel light yellow
> color sel lemon chiffon
> color sel light yellow
> color sel light goldenrod yellow
> color sel light yellow
> name frozen 4v8q_30S sel
registering illegal selector name "4v8q_30S"
> name frozen 4v8q_30S sel
registering illegal selector name "4v8q_30S"
> toolshed show
> select clear
> select #1/m:59
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
90 atoms, 92 bonds, 12 residues, 1 model selected
> select up
1147 atoms, 1163 bonds, 151 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light yellow
> select clear
> select #1/t:39
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
60 atoms, 59 bonds, 8 residues, 1 model selected
> select up
971 atoms, 987 bonds, 125 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light yellow
> select clear
> select #1/2:13
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
68 atoms, 69 bonds, 7 residues, 1 model selected
> select up
209 atoms, 213 bonds, 25 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light yellow
> select clear
> select #1/4:53
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/3:53
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
4753 atoms, 5288 bonds, 235 residues, 1 model selected
> select up
8784 atoms, 9396 bonds, 741 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/5:16
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
104 atoms, 116 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> select #1
145317 atoms, 157758 bonds, 10674 residues, 1 model selected
> show sel surfaces
> select clear
> hide sel cartoons
> select clear
Drag select of 4v8q_withEF-Tu.pdb_A SES surface, 4v8q_withEF-Tu.pdb_B SES
surface, 112696 of 112796 triangles, 4v8q_withEF-Tu.pdb_C SES surface,
4v8q_withEF-Tu.pdb_D SES surface, 4v8q_withEF-Tu.pdb_E SES surface, 29 of
62142 triangles, 4v8q_withEF-Tu.pdb_F SES surface, 4v8q_withEF-Tu.pdb_G SES
surface, 65085 of 65362 triangles, 4v8q_withEF-Tu.pdb_H SES surface,
4v8q_withEF-Tu.pdb_I SES surface, 4v8q_withEF-Tu.pdb_J SES surface,
4v8q_withEF-Tu.pdb_K SES surface, 5776261 of 7461216 triangles, 4v8q_withEF-
Tu.pdb_L SES surface, 323861 of 328776 triangles, 4v8q_withEF-Tu.pdb_M SES
surface, 39768 of 218474 triangles, 4v8q_withEF-Tu.pdb_N SES surface, 38637 of
291894 triangles, 4v8q_withEF-Tu.pdb_O SES surface, 4v8q_withEF-Tu.pdb_P SES
surface, 4v8q_withEF-Tu.pdb_Q SES surface, 28176 of 201808 triangles,
4v8q_withEF-Tu.pdb_R SES surface, 171914 of 178924 triangles, 4v8q_withEF-
Tu.pdb_S SES surface, 93863 of 125096 triangles, 4v8q_withEF-Tu.pdb_U SES
surface, 4v8q_withEF-Tu.pdb_V SES surface, 25123 of 110370 triangles,
4v8q_withEF-Tu.pdb_W SES surface, 4v8q_withEF-Tu.pdb_X SES surface, 146966 of
153360 triangles, 4v8q_withEF-Tu.pdb_Y SES surface, 4v8q_withEF-Tu.pdb_Z SES
surface, 4v8q_withEF-Tu.pdb_a SES surface, 63043 of 170520 triangles,
4v8q_withEF-Tu.pdb_b SES surface, 4v8q_withEF-Tu.pdb_c SES surface,
4v8q_withEF-Tu.pdb_d SES surface, 4v8q_withEF-Tu.pdb_e SES surface,
4v8q_withEF-Tu.pdb_f SES surface, 4v8q_withEF-Tu.pdb_g SES surface, 174238 of
207322 triangles, 5153 residues
> select up
73760 atoms, 80366 bonds, 5156 residues, 34 models selected
> select up
89456 atoms, 97659 bonds, 6169 residues, 34 models selected
> select up
93828 atoms, 102106 bonds, 6773 residues, 34 models selected
> color (#!1 & sel) dark gray
> select ~sel
674664 atoms, 731455 bonds, 10 pseudobonds, 50011 residues, 8 models selected
> ui tool show "Color Actions"
> color sel light yellow
> color sel lemon chiffon
> color sel pale goldenrod
> color sel lemon chiffon
> select clear
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!2 models
> hide #!2 models
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> open C:/Users/claud/Downloads/4v8q-pdb-bundle.tar/4v8q-pdb-
> bundle/4v8q_withEF-Tu.pdb
Summary of feedback from opening C:/Users/claud/Downloads/4v8q-pdb-
bundle.tar/4v8q-pdb-bundle/4v8q_withEF-Tu.pdb
---
warning | Ignored bad PDB record found on line 155403
END
Chain information for 4v8q_withEF-Tu.pdb #6
---
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> hide #!1 models
> select #6/7:208@OE2
1 atom, 1 residue, 1 model selected
> select up
102 atoms, 107 bonds, 6 residues, 1 model selected
> select up
4883 atoms, 5433 bonds, 244 residues, 1 model selected
> select up
8888 atoms, 9512 bonds, 746 residues, 1 model selected
> select ~sel
913809 atoms, 991319 bonds, 10 pseudobonds, 67458 residues, 9 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> show #5 models
> show #!4 models
> show #!3 models
> ~select #1
623175 atoms, 675803 bonds, 10 pseudobonds, 46110 residues, 61 models selected
> ~select #2
466566 atoms, 506003 bonds, 8 pseudobonds, 34492 residues, 5 models selected
> ~select #3
309047 atoms, 334989 bonds, 2 pseudobonds, 23014 residues, 3 models selected
> ~select #4
155169 atoms, 168230 bonds, 11529 residues, 1 model selected
> ~select #5
Nothing selected
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #5 models
> show #!1 models
> hide #!1 models
> select #6/4:47@O6
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1640 atoms, 1832 bonds, 77 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> select #6/3:46@OP2
1 atom, 1 residue, 1 model selected
> select #6/3:45@O2'
1 atom, 1 residue, 1 model selected
> select #6/3:48@OP2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1640 atoms, 1832 bonds, 77 residues, 1 model selected
> color sel forest green
> select #6
8888 atoms, 9512 bonds, 4 pseudobonds, 746 residues, 2 models selected
> show sel surfaces
> hide sel atoms
> ~select #6
6 models selected
> select #6/4:45@OP1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel pink
> color sel light pink
> color sel peach puff
> color sel navajo white
> color sel peach puff
> color sel light pink
> color sel thistle
> color sel plum
> color sel pale violet red
> color sel orchid
> color sel crimson
> color sel tomato
> color sel crimson
> color sel light coral
> color sel yellow
> show #!1 models
> hide #!1 models
> color sel indian red
> color sel yellow
> select #6/3:22@N6
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel forest green
> select up
8888 atoms, 9512 bonds, 746 residues, 2 models selected
> select up
8888 atoms, 9512 bonds, 4 pseudobonds, 746 residues, 8 models selected
> select up
8888 atoms, 9512 bonds, 4 pseudobonds, 746 residues, 8 models selected
> select clear
> select #6/7:127@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
113 atoms, 114 bonds, 14 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> color sel deep sky blue
> color sel sky blue
> color sel light sky blue
> color sel aquamarine
> color sel burly wood
> color sel powder blue
> color sel pale violet red
> color sel light coral
> color sel plum
> color sel peach puff
> color sel pink
> color sel navajo white
> color sel sandy brown
> color sel coral
> color sel light coral
> select #6/6:24@O6
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1305 atoms, 1454 bonds, 62 residues, 2 models selected
> color sel cornflower blue
> select #6/h:91@O
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
112 atoms, 112 bonds, 13 residues, 2 models selected
> select up
1184 atoms, 1203 bonds, 144 residues, 2 models selected
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel light steel blue
> color sel powder blue
> color sel dodger blue
> color sel royal blue
> color sel indigo
> color sel navy
> color sel dark blue
> color sel medium blue
> color sel blue
> color sel rebecca purple
> color sel medium orchid
> color sel purple
> color sel medium purple
> color sel purple
> color sel dark magenta
> color sel dark orchid
> color sel medium violet red
> color sel orchid
> color sel light sea green
> color sel medium turquoise
> color sel turquoise
> color sel dodger blue
> color sel medium spring green
> color sel dark turquoise
> color sel deep sky blue
> color sel dark sea green
> color sel light blue
> color sel light pink
> color sel pale violet red
> color sel medium purple
> color sel purple
> color sel medium purple
> select clear
> select #6/5:18@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
104 atoms, 116 bonds, 5 residues, 2 models selected
> color sel cyan
> color sel deep sky blue
> color sel cyan
> color sel deep sky blue
> select clear
> select #6/4:45@C5'
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel goldenrod
> color sel sandy brown
> color sel peach puff
> color sel cadet blue
> color sel steel blue
> color sel light slate gray
> color sel cadet blue
> color sel slate gray
> color sel light slate gray
> color sel cadet blue
> color sel steel blue
> color sel orange
> color sel indian red
> color sel crimson
> color sel sandy brown
> color sel light pink
> color sel chocolate
> color sel brown
> color sel crimson
> color sel fire brick
> select clear
> select #6/7:213@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
157 atoms, 162 bonds, 19 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> color sel dark salmon
> color sel salmon
> color sel light salmon
> color sel indian red
> color sel light sea green
> color sel medium turquoise
> color sel light sea green
> color sel indigo
> color sel aquamarine
> color sel light slate gray
> color sel cadet blue
> color sel dodger blue
> color sel dark cyan
> color sel medium aquamarine
> color sel light sky blue
> color sel pale violet red
> select #6/4:24@C5
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select down
1 atom, 1 residue, 2 models selected
> select clear
> select #6/7:130@CD2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
41 atoms, 42 bonds, 5 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> color sel medium slate blue
> color sel rebecca purple
> color sel midnight blue
> color sel medium turquoise
> color sel steel blue
> color sel dark turquoise
> color sel royal blue
> color sel slate blue
> color sel purple
> color sel dark magenta
> color sel tan
> color sel rosy brown
> color sel teal
> select #6/6:24@N3
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1305 atoms, 1454 bonds, 62 residues, 2 models selected
> color sel royal blue
> select #6/7:321@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
59 atoms, 60 bonds, 7 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> color sel dark turquoise
> color sel medium turquoise
> color sel teal
> color sel light sea green
> color (#!6 & sel) #00aa7fff
> color (#!6 & sel) #aa0000ff
> color (#!6 & sel) #ffff7fff
> color (#!6 & sel) #aaaaffff
> color sel medium turquoise
> color sel light sea green
> select clear
> select #6/4:47@O6
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> select up
8888 atoms, 9512 bonds, 746 residues, 2 models selected
> color sel chocolate
> select clear
> select #6/4:48@O5'
1 atom, 1 residue, 1 model selected
> select #6/5:18@C6
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
104 atoms, 116 bonds, 5 residues, 2 models selected
> color sel deep sky blue
> select #6/3:28@O2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel forest green
> select #6/h:139@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
92 atoms, 91 bonds, 11 residues, 2 models selected
> select up
1184 atoms, 1203 bonds, 144 residues, 2 models selected
> color sel aquamarine
> color sel medium aquamarine
> color sel medium purple
> select #6/6:40@N4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
1305 atoms, 1454 bonds, 62 residues, 2 models selected
> color sel royal blue
> select #6/7:367@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
64 atoms, 64 bonds, 8 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> color sel sky blue
> color sel aquamarine
> color sel sky blue
> color sel pale green
> color sel sky blue
> color sel steel blue
> color sel light sea green
> color sel sky blue
> color sel light blue
> color sel light sky blue
> color sel powder blue
> color sel dark slate gray
> color sel cadet blue
> color sel steel blue
> color sel medium turquoise
> color sel light sea green
> color sel medium turquoise
> color sel dark khaki
> color sel salmon
> color sel light salmon
> color sel dark salmon
> color sel yellow
> color sel gold
> color sel green yellow
> color sel sandy brown
> color sel misty rose
> color sel papaya whip
> color sel cornsilk
> color sel peach puff
> color sel honeydew
> color sel pale turquoise
> color sel powder blue
> color sel dark sea green
> color sel rosy brown
> color sel pale violet red
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> select clear
> show #!1 models
> hide #!1 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting soft
> set bgColor white
> view
> view
> show #!1 models
> view
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> ui tool show "Side View"
> hide #!1 models
> view 1
Expected an objects specifier or a view name or a keyword
> view list
No named views.
> view list
No named views.
> view list
No named views.
> view 1
Expected an objects specifier or a view name or a keyword
> view 1
Expected an objects specifier or a view name or a keyword
> view 1
Expected an objects specifier or a view name or a keyword
> view list
No named views.
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> view 1, save
Expected an objects specifier or a view name or a keyword
> view 1, save
Expected an objects specifier or a view name or a keyword
> view 1, save
Expected an objects specifier or a view name or a keyword
> safe view 1
Unknown command: safe view 1
> view
> view list
No named views.
> view list
No named views.
> view list
No named views.
> view
> hide #!6 models
> show #!1 models
> view 1
Expected an objects specifier or a view name or a keyword
> view
> show #!6 models
> hide #!1 models
> view #1, store
Expected an objects specifier or a view name or a keyword
> view #1, save
Expected an objects specifier or a view name or a keyword
> view #1
> show #!1 models
> hide #!1 models
> view #2
> view
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!2 models
> select #2
156609 atoms, 169800 bonds, 2 pseudobonds, 11618 residues, 2 models selected
> show sel surfaces
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> select #2/4:253@O2
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select #2
156609 atoms, 169800 bonds, 2 pseudobonds, 11618 residues, 2 models selected
> ~select #2
60 models selected
> select #2
156609 atoms, 169800 bonds, 2 pseudobonds, 11618 residues, 2 models selected
> hide sel surfaces
> hide sel atoms
> select clear
> select #2/8:65
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> hide #!2 cartoons
> show #!2 surfaces
> select #2/4:268@C2'
1 atom, 1 residue, 1 model selected
> ui mousemode right rotate
> select up
63 atoms, 67 bonds, 3 residues, 4 models selected
> select up
10416 atoms, 11644 bonds, 488 residues, 4 models selected
> show sel cartoons
> hide sel surfaces
> color (#!2 & sel) red
> select ~sel
766964 atoms, 831429 bonds, 12 pseudobonds, 57042 residues, 46 models selected
> select ~sel
10416 atoms, 11644 bonds, 2 pseudobonds, 488 residues, 2 models selected
> select ~sel
766964 atoms, 831429 bonds, 12 pseudobonds, 57042 residues, 46 models selected
> show sel & #!2 cartoons
> hide sel & #!2 surfaces
> select clear
> select #2/5:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 6 residues, 2 models selected
> select up
1170 atoms, 1191 bonds, 145 residues, 2 models selected
> color (#!2 & sel) red
> select #2/4:322
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10467 atoms, 11694 bonds, 494 residues, 5 models selected
> select up
11591 atoms, 12835 bonds, 638 residues, 5 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
opened ChimeraX session
Drag select of 4888 residues
> select up
86528 atoms, 94589 bonds, 5803 residues, 32 models selected
> color (#!2 & sel) dark gray
> select ~sel
679261 atoms, 735649 bonds, 12 pseudobonds, 51089 residues, 9 models selected
> ui tool show "Side View"
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> select #2/P:61
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
155 atoms, 156 bonds, 19 residues, 2 models selected
> select up
1897 atoms, 1922 bonds, 244 residues, 3 models selected
> select up
145018 atoms, 156965 bonds, 10980 residues, 3 models selected
> select down
1897 atoms, 1922 bonds, 244 residues, 57 models selected
> select up
2025 atoms, 2050 bonds, 260 residues, 4 models selected
> select up
3827 atoms, 3875 bonds, 502 residues, 5 models selected
> color sel dark gray
> select clear
> show #!2 surfaces
> hide #!2 cartoons
Drag select of 6q97_A-site.pdb_1 SES surface, 7095268 of 7969538 triangles,
6q97_A-site.pdb_2 SES surface, 65767 of 4256176 triangles, 6q97_A-site.pdb_3
SES surface, 350150 of 350468 triangles, 6q97_A-site.pdb_6 SES surface,
6q97_A-site.pdb_B SES surface, 280804 of 295732 triangles, 6q97_A-site.pdb_C
SES surface, 216075 of 231886 triangles, 6q97_A-site.pdb_D SES surface,
6q97_A-site.pdb_E SES surface, 156585 of 190010 triangles, 6q97_A-site.pdb_F
SES surface, 95125 of 189188 triangles, 6q97_A-site.pdb_G SES surface, 6q97_A-
site.pdb_H SES surface, 19557 of 153748 triangles, 6q97_A-site.pdb_J SES
surface, 6q97_A-site.pdb_K SES surface, 6110 of 121150 triangles, 6q97_A-
site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 143366 of 152098
triangles, 6q97_A-site.pdb_N SES surface, 6q97_A-site.pdb_O SES surface,
6q97_A-site.pdb_P SES surface, 18187 of 137720 triangles, 6q97_A-site.pdb_Q
SES surface, 6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface,
6q97_A-site.pdb_T SES surface, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_X SES
surface, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface, 6q97_A-
site.pdb_a SES surface, 38933 of 93508 triangles, 6q97_A-site.pdb_b SES
surface, 6q97_A-site.pdb_c SES surface, 6q97_A-site.pdb_d SES surface, 6q97_A-
site.pdb_e SES surface, 6q97_A-site.pdb_f SES surface, 33479 of 47780
triangles, 6q97_A-site.pdb_k SES surface, 20176 of 110942 triangles, 6q97_A-
site.pdb_p SES surface, 24581 of 123830 triangles
Drag select of 6q97_A-site.pdb_1 SES surface, 4105436 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 248904 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 29411 of 33600 triangles, 6q97_A-site.pdb_C SES surface, 225505
of 231886 triangles, 6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_E SES
surface, 8839 of 190010 triangles, 6q97_A-site.pdb_F SES surface, 188089 of
189188 triangles, 6q97_A-site.pdb_H SES surface, 6q97_A-site.pdb_I SES
surface, 121026 of 172054 triangles, 6q97_A-site.pdb_J SES surface, 6q97_A-
site.pdb_K SES surface, 16325 of 121150 triangles, 6q97_A-site.pdb_L SES
surface, 187975 of 188938 triangles, 6q97_A-site.pdb_M SES surface, 149731 of
152098 triangles, 6q97_A-site.pdb_N SES surface, 116275 of 127082 triangles,
6q97_A-site.pdb_O SES surface, 86799 of 121204 triangles, 6q97_A-site.pdb_P
SES surface, 47679 of 137720 triangles, 6q97_A-site.pdb_Q SES surface, 6q97_A-
site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES
surface, 31867 of 112872 triangles, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 80160 of 84440
triangles, 6q97_A-site.pdb_Y SES surface, 50738 of 74596 triangles, 6q97_A-
site.pdb_Z SES surface, 6q97_A-site.pdb_b SES surface, 6q97_A-site.pdb_c SES
surface, 3130 of 63158 triangles, 6q97_A-site.pdb_d SES surface, 8817 of 68556
triangles, 6q97_A-site.pdb_e SES surface, 76713 of 88192 triangles, 6q97_A-
site.pdb_f SES surface
> select up
56368 atoms, 4510 residues, 57 models selected
> select down
Nothing selected
Drag select of 6q97_A-site.pdb_1 SES surface, 4471686 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 315111 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 33506 of 33600 triangles, 6q97_A-site.pdb_C SES surface, 229148
of 231886 triangles, 6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_E SES
surface, 36992 of 190010 triangles, 6q97_A-site.pdb_F SES surface, 6q97_A-
site.pdb_H SES surface, 6q97_A-site.pdb_I SES surface, 152262 of 172054
triangles, 6q97_A-site.pdb_J SES surface, 6q97_A-site.pdb_K SES surface, 33182
of 121150 triangles, 6q97_A-site.pdb_L SES surface, 6q97_A-site.pdb_M SES
surface, 6q97_A-site.pdb_N SES surface, 122324 of 127082 triangles, 6q97_A-
site.pdb_O SES surface, 114932 of 121204 triangles, 6q97_A-site.pdb_P SES
surface, 58145 of 137720 triangles, 6q97_A-site.pdb_Q SES surface, 6q97_A-
site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES
surface, 47704 of 112872 triangles, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_Y SES
surface, 61268 of 74596 triangles, 6q97_A-site.pdb_Z SES surface, 6q97_A-
site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 12611 of 63158
triangles, 6q97_A-site.pdb_d SES surface, 15707 of 68556 triangles, 6q97_A-
site.pdb_e SES surface, 85681 of 88192 triangles, 6q97_A-site.pdb_f SES
surface
Drag select of 6q97_A-site.pdb_1 SES surface, 2369943 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 250073 of 350468 triangles, 6q97_A-site.pdb_C
SES surface, 192958 of 231886 triangles, 6q97_A-site.pdb_D SES surface, 124353
of 235976 triangles, 6q97_A-site.pdb_E SES surface, 1217 of 190010 triangles,
6q97_A-site.pdb_F SES surface, 187378 of 189188 triangles, 6q97_A-site.pdb_H
SES surface, 6q97_A-site.pdb_I SES surface, 153753 of 172054 triangles,
6q97_A-site.pdb_J SES surface, 6q97_A-site.pdb_L SES surface, 46907 of 188938
triangles, 6q97_A-site.pdb_M SES surface, 91747 of 152098 triangles, 6q97_A-
site.pdb_N SES surface, 30844 of 127082 triangles, 6q97_A-site.pdb_O SES
surface, 43460 of 121204 triangles, 6q97_A-site.pdb_P SES surface, 20004 of
137720 triangles, 6q97_A-site.pdb_Q SES surface, 140704 of 143740 triangles,
6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface, 91480 of 122990
triangles, 6q97_A-site.pdb_U SES surface, 54637 of 116360 triangles, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 41670 of 84440
triangles, 6q97_A-site.pdb_Z SES surface, 6q97_A-site.pdb_b SES surface, 72796
of 76920 triangles, 6q97_A-site.pdb_e SES surface, 874 of 88192 triangles,
6q97_A-site.pdb_f SES surface
> color sel dark gray
> select clear
> select #2/a:45@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
216 atoms, 220 bonds, 29 residues, 2 models selected
> select up
523 atoms, 531 bonds, 67 residues, 2 models selected
> color sel dark gray
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> select clear
> select clear
> select #2/B:115@CB
1 atom, 1 residue, 1 model selected
> set bgColor black
> select up
16 atoms, 14 bonds, 2 residues, 3 models selected
> select up
47 atoms, 45 bonds, 6 residues, 3 models selected
> select up
3191 atoms, 3239 bonds, 421 residues, 3 models selected
> color sel dark gray
> lighting soft
> lighting simple
> lighting full
> lighting soft
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> open C:/Users/claud/Downloads/6q97-pdb-bundle.tar/6q97_A-site.pdb
Summary of feedback from opening C:/Users/claud/Downloads/6q97-pdb-
bundle.tar/6q97_A-site.pdb
---
warning | Ignored bad PDB record found on line 157976
END
Chain information for 6q97_A-site.pdb #7
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
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l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select #7/4:304@C1'
1 atom, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> select clear
> hide #!2 models
> select up
77 atoms, 81 bonds, 4 residues, 1 model selected
> select up
10771 atoms, 12004 bonds, 535 residues, 1 model selected
> select up
10782 atoms, 12014 bonds, 536 residues, 1 model selected
> select up
10908 atoms, 12145 bonds, 552 residues, 1 model selected
> select clear
> show #!7 cartoons
> hide #!7 surfaces
> hide #!7 atoms
> select up
10595 atoms, 11836 bonds, 500 residues, 1 model selected
> select up
11719 atoms, 12977 bonds, 644 residues, 1 model selected
> select ~sel
910679 atoms, 987061 bonds, 12 pseudobonds, 67866 residues, 10 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/9:7
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
128 atoms, 142 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> select #7/7:29
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1644 atoms, 1836 bonds, 77 residues, 1 model selected
> color sel forest green
> select #7/4:319
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
7134 atoms, 7978 bonds, 334 residues, 1 model selected
> color sel cornflower blue
> color sel royal blue
> select clear
> select #7/5:104
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 4 residues, 1 model selected
> select up
1170 atoms, 1191 bonds, 145 residues, 1 model selected
> color sel medium purple
> select clear
> show #!6 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> select clear
> select #7/8:53
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1638 atoms, 1830 bonds, 77 residues, 1 model selected
> select up
1640 atoms, 1830 bonds, 79 residues, 1 model selected
> color sel light pink
> color sel light coral
> color sel indian red
> color sel orange red
> color sel indian red
> select clear
> hide #!7 models
> show #!6 models
> select #6/h:143@CD
1 atom, 1 residue, 1 model selected
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9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
92 atoms, 91 bonds, 11 residues, 2 models selected
> select up
1184 atoms, 1203 bonds, 144 residues, 2 models selected
> color sel medium purple
> select #6/6:23@OP2
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1305 atoms, 1454 bonds, 62 residues, 2 models selected
> color sel royal blue
> select #6/7:399@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
76 atoms, 75 bonds, 11 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> color sel light sky blue
> color sel light steel blue
> color sel sky blue
> color sel aquamarine
> color sel medium turquoise
> color sel turquoise
> color sel light sea green
> color sel medium turquoise
> select #6/5:14@N1
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 21 bonds, 1 residue, 2 models selected
> select up
104 atoms, 116 bonds, 5 residues, 2 models selected
> color sel deep sky blue
> select #6/3:30@N3
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel forest green
> select #6/4:45@C1'
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel indian red
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!7 models
> hide #!6 models
> select #7
11719 atoms, 12977 bonds, 2 pseudobonds, 644 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> show sel cartoons
> select clear
> select #7/4:226@N1
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
7134 atoms, 7978 bonds, 334 residues, 2 models selected
> color sel royal blue
> select #7/5:28@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
35 atoms, 34 bonds, 4 residues, 2 models selected
> select up
1170 atoms, 1191 bonds, 145 residues, 2 models selected
> color sel medium purple
> select #7/7:26@N4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
1644 atoms, 1836 bonds, 77 residues, 2 models selected
> color sel forest green
> select #7/8:26@N4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
1638 atoms, 1830 bonds, 77 residues, 2 models selected
> color sel indian red
> select #7/9:2@N3
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
128 atoms, 142 bonds, 6 residues, 2 models selected
> color sel deep sky blue
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> hide #!7 models
> show #!1 models
> view
Drag select of 4v8q_withEF-Tu.pdb_A SES surface, 75024 of 98156 triangles,
4v8q_withEF-Tu.pdb_B SES surface, 99174 of 112796 triangles, 4v8q_withEF-
Tu.pdb_C SES surface, 4v8q_withEF-Tu.pdb_D SES surface, 4v8q_withEF-Tu.pdb_F
SES surface, 4v8q_withEF-Tu.pdb_G SES surface, 18206 of 65362 triangles,
4v8q_withEF-Tu.pdb_H SES surface, 4v8q_withEF-Tu.pdb_I SES surface, 82175 of
85306 triangles, 4v8q_withEF-Tu.pdb_J SES surface, 5667 of 45694 triangles,
4v8q_withEF-Tu.pdb_K SES surface, 4712391 of 7461216 triangles, 4v8q_withEF-
Tu.pdb_L SES surface, 154948 of 328776 triangles, 4v8q_withEF-Tu.pdb_N SES
surface, 4631 of 291894 triangles, 4v8q_withEF-Tu.pdb_O SES surface, 190800 of
213010 triangles, 4v8q_withEF-Tu.pdb_P SES surface, 216512 of 225352
triangles, 4v8q_withEF-Tu.pdb_R SES surface, 96603 of 178924 triangles,
4v8q_withEF-Tu.pdb_U SES surface, 4v8q_withEF-Tu.pdb_W SES surface,
4v8q_withEF-Tu.pdb_X SES surface, 14445 of 153360 triangles, 4v8q_withEF-
Tu.pdb_Y SES surface, 4v8q_withEF-Tu.pdb_Z SES surface, 63310 of 113566
triangles, 4v8q_withEF-Tu.pdb_a SES surface, 21967 of 170520 triangles,
4v8q_withEF-Tu.pdb_b SES surface, 4v8q_withEF-Tu.pdb_c SES surface,
4v8q_withEF-Tu.pdb_d SES surface, 4v8q_withEF-Tu.pdb_e SES surface,
4v8q_withEF-Tu.pdb_f SES surface, 119345 of 123866 triangles, 4v8q_withEF-
Tu.pdb_g SES surface, 70364 of 207322 triangles, 4039 residues
Drag select of 4v8q_withEF-Tu.pdb_A SES surface, 4v8q_withEF-Tu.pdb_B SES
surface, 4v8q_withEF-Tu.pdb_C SES surface, 4v8q_withEF-Tu.pdb_D SES surface,
4v8q_withEF-Tu.pdb_E SES surface, 5835 of 62142 triangles, 4v8q_withEF-
Tu.pdb_F SES surface, 4v8q_withEF-Tu.pdb_G SES surface, 4v8q_withEF-Tu.pdb_H
SES surface, 4v8q_withEF-Tu.pdb_I SES surface, 4v8q_withEF-Tu.pdb_J SES
surface, 4v8q_withEF-Tu.pdb_K SES surface, 6306290 of 7461216 triangles,
4v8q_withEF-Tu.pdb_L SES surface, 4v8q_withEF-Tu.pdb_M SES surface, 111794 of
218474 triangles, 4v8q_withEF-Tu.pdb_N SES surface, 107530 of 291894
triangles, 4v8q_withEF-Tu.pdb_O SES surface, 4v8q_withEF-Tu.pdb_P SES surface,
4v8q_withEF-Tu.pdb_Q SES surface, 85475 of 201808 triangles, 4v8q_withEF-
Tu.pdb_R SES surface, 4v8q_withEF-Tu.pdb_S SES surface, 123951 of 125096
triangles, 4v8q_withEF-Tu.pdb_T SES surface, 6801 of 138540 triangles,
4v8q_withEF-Tu.pdb_U SES surface, 4v8q_withEF-Tu.pdb_V SES surface, 46678 of
110370 triangles, 4v8q_withEF-Tu.pdb_W SES surface, 4v8q_withEF-Tu.pdb_X SES
surface, 152959 of 153360 triangles, 4v8q_withEF-Tu.pdb_Y SES surface,
4v8q_withEF-Tu.pdb_Z SES surface, 4v8q_withEF-Tu.pdb_a SES surface, 110754 of
170520 triangles, 4v8q_withEF-Tu.pdb_b SES surface, 4v8q_withEF-Tu.pdb_c SES
surface, 4v8q_withEF-Tu.pdb_d SES surface, 4v8q_withEF-Tu.pdb_e SES surface,
4v8q_withEF-Tu.pdb_f SES surface, 4v8q_withEF-Tu.pdb_g SES surface, 199200 of
207322 triangles, 4v8q_withEF-Tu.pdb_i SES surface, 1577 of 3905368 triangles,
5768 residues
> select up
91025 atoms, 99252 bonds, 6368 residues, 34 models selected
> show #!2 models
> hide #!2 models
> select up
93828 atoms, 102106 bonds, 6773 residues, 34 models selected
> color sel dark gray
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!3 models
> hide #!1 models
> select #3/V:260
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
8875 atoms, 9910 bonds, 424 residues, 1 model selected
> select up
14983 atoms, 16135 bonds, 1200 residues, 1 model selected
> select up
47978 atoms, 53079 bonds, 2738 residues, 1 model selected
> select down
15006 atoms, 16135 bonds, 1201 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!3 cartoons
> show #!3 surfaces
> hide #!3 atoms
Drag select of 4v6t_withEF-G.pdb_A SES surface, 434 of 3958492 triangles,
4v6t_withEF-G.pdb_f SES surface, 6458052 of 7355268 triangles,
4v6t_withEF-G.pdb_g SES surface, 172107 of 275862 triangles,
4v6t_withEF-G.pdb_h SES surface, 4v6t_withEF-G.pdb_i SES surface,
4v6t_withEF-G.pdb_j SES surface, 109174 of 167524 triangles,
4v6t_withEF-G.pdb_k SES surface, 152564 of 168342 triangles,
4v6t_withEF-G.pdb_l SES surface, 153822 of 154734 triangles,
4v6t_withEF-G.pdb_n SES surface, 4v6t_withEF-G.pdb_o SES surface, 43086 of
112616 triangles, 4v6t_withEF-G.pdb_p SES surface, 4v6t_withEF-G.pdb_q SES
surface, 142485 of 143310 triangles, 4v6t_withEF-G.pdb_r SES surface,
4v6t_withEF-G.pdb_s SES surface, 4v6t_withEF-G.pdb_t SES surface, 70477 of
127746 triangles, 4v6t_withEF-G.pdb_u SES surface, 4v6t_withEF-G.pdb_v SES
surface, 4v6t_withEF-G.pdb_w SES surface, 4v6t_withEF-G.pdb_x SES surface,
4v6t_withEF-G.pdb_y SES surface, 4v6t_withEF-G.pdb_z SES surface,
4v6t_withEF-G.pdb_0 SES surface, 4v6t_withEF-G.pdb_1 SES surface,
4v6t_withEF-G.pdb_2 SES surface, 4v6t_withEF-G.pdb_3 SES surface,
4v6t_withEF-G.pdb_Z SES surface, 4v6t_withEF-G.pdb_a SES surface,
4v6t_withEF-G.pdb_b SES surface, 4v6t_withEF-G.pdb_c SES surface,
4v6t_withEF-G.pdb_d SES surface, 4v6t_withEF-G.pdb_e SES surface
Drag select of 4v6t_withEF-G.pdb_A SES surface, 28955 of 3958492 triangles,
4v6t_withEF-G.pdb_F SES surface, 429 of 104002 triangles, 4v6t_withEF-G.pdb_K
SES surface, 5463 of 114982 triangles, 4v6t_withEF-G.pdb_f SES surface,
6600429 of 7355268 triangles, 4v6t_withEF-G.pdb_g SES surface, 263319 of
275862 triangles, 4v6t_withEF-G.pdb_h SES surface, 202893 of 207708 triangles,
4v6t_withEF-G.pdb_i SES surface, 4v6t_withEF-G.pdb_j SES surface, 93324 of
167524 triangles, 4v6t_withEF-G.pdb_k SES surface, 95654 of 168342 triangles,
4v6t_withEF-G.pdb_l SES surface, 4v6t_withEF-G.pdb_n SES surface,
4v6t_withEF-G.pdb_o SES surface, 22595 of 112616 triangles,
4v6t_withEF-G.pdb_p SES surface, 4v6t_withEF-G.pdb_q SES surface, 129916 of
143310 triangles, 4v6t_withEF-G.pdb_r SES surface, 4v6t_withEF-G.pdb_s SES
surface, 4v6t_withEF-G.pdb_t SES surface, 50210 of 127746 triangles,
4v6t_withEF-G.pdb_u SES surface, 4v6t_withEF-G.pdb_v SES surface,
4v6t_withEF-G.pdb_w SES surface, 4v6t_withEF-G.pdb_x SES surface,
4v6t_withEF-G.pdb_y SES surface, 4v6t_withEF-G.pdb_z SES surface,
4v6t_withEF-G.pdb_0 SES surface, 4v6t_withEF-G.pdb_1 SES surface,
4v6t_withEF-G.pdb_2 SES surface, 4v6t_withEF-G.pdb_3 SES surface,
4v6t_withEF-G.pdb_Z SES surface, 4v6t_withEF-G.pdb_a SES surface,
4v6t_withEF-G.pdb_b SES surface, 4v6t_withEF-G.pdb_c SES surface,
4v6t_withEF-G.pdb_d SES surface, 33585 of 44032 triangles, 4v6t_withEF-G.pdb_e
SES surface
> select clear
Drag select of 4v6t_withEF-G.pdb_f SES surface, 4540039 of 7355268 triangles,
4v6t_withEF-G.pdb_g SES surface, 16322 of 275862 triangles,
4v6t_withEF-G.pdb_h SES surface, 100870 of 207708 triangles,
4v6t_withEF-G.pdb_i SES surface, 4v6t_withEF-G.pdb_k SES surface, 11424 of
168342 triangles, 4v6t_withEF-G.pdb_l SES surface, 153522 of 154734 triangles,
4v6t_withEF-G.pdb_n SES surface, 135235 of 138936 triangles,
4v6t_withEF-G.pdb_p SES surface, 4v6t_withEF-G.pdb_q SES surface, 11003 of
143310 triangles, 4v6t_withEF-G.pdb_r SES surface, 99688 of 117632 triangles,
4v6t_withEF-G.pdb_s SES surface, 98362 of 110164 triangles,
4v6t_withEF-G.pdb_u SES surface, 4v6t_withEF-G.pdb_v SES surface,
4v6t_withEF-G.pdb_w SES surface, 4v6t_withEF-G.pdb_x SES surface,
4v6t_withEF-G.pdb_y SES surface, 4v6t_withEF-G.pdb_z SES surface, 54991 of
92118 triangles, 4v6t_withEF-G.pdb_0 SES surface, 75444 of 81516 triangles,
4v6t_withEF-G.pdb_1 SES surface, 4v6t_withEF-G.pdb_2 SES surface,
4v6t_withEF-G.pdb_3 SES surface, 4v6t_withEF-G.pdb_Z SES surface,
4v6t_withEF-G.pdb_a SES surface, 43019 of 56210 triangles, 4v6t_withEF-G.pdb_b
SES surface, 4v6t_withEF-G.pdb_c SES surface, 4v6t_withEF-G.pdb_e SES surface,
185752 of 326338 triangles
> select clear
Drag select of 4v6t_withEF-G.pdb_A SES surface, 1774 of 3958492 triangles,
4v6t_withEF-G.pdb_f SES surface, 6238400 of 7355268 triangles,
4v6t_withEF-G.pdb_g SES surface, 190662 of 275862 triangles,
4v6t_withEF-G.pdb_h SES surface, 201467 of 207708 triangles,
4v6t_withEF-G.pdb_i SES surface, 4v6t_withEF-G.pdb_j SES surface, 63200 of
167524 triangles, 4v6t_withEF-G.pdb_k SES surface, 98609 of 168342 triangles,
4v6t_withEF-G.pdb_l SES surface, 4v6t_withEF-G.pdb_n SES surface,
4v6t_withEF-G.pdb_o SES surface, 11338 of 112616 triangles,
4v6t_withEF-G.pdb_p SES surface, 4v6t_withEF-G.pdb_q SES surface, 124448 of
143310 triangles, 4v6t_withEF-G.pdb_r SES surface, 4v6t_withEF-G.pdb_s SES
surface, 4v6t_withEF-G.pdb_t SES surface, 36676 of 127746 triangles,
4v6t_withEF-G.pdb_u SES surface, 4v6t_withEF-G.pdb_v SES surface,
4v6t_withEF-G.pdb_w SES surface, 4v6t_withEF-G.pdb_x SES surface,
4v6t_withEF-G.pdb_y SES surface, 4v6t_withEF-G.pdb_z SES surface,
4v6t_withEF-G.pdb_0 SES surface, 4v6t_withEF-G.pdb_1 SES surface,
4v6t_withEF-G.pdb_2 SES surface, 4v6t_withEF-G.pdb_3 SES surface,
4v6t_withEF-G.pdb_Z SES surface, 4v6t_withEF-G.pdb_a SES surface,
4v6t_withEF-G.pdb_b SES surface, 4v6t_withEF-G.pdb_c SES surface,
4v6t_withEF-G.pdb_d SES surface, 32956 of 44032 triangles, 4v6t_withEF-G.pdb_e
SES surface
Drag select of 4v6t_withEF-G.pdb_f SES surface, 4687153 of 7355268 triangles,
4v6t_withEF-G.pdb_g SES surface, 14909 of 275862 triangles,
4v6t_withEF-G.pdb_h SES surface, 138492 of 207708 triangles,
4v6t_withEF-G.pdb_i SES surface, 4v6t_withEF-G.pdb_k SES surface, 37095 of
168342 triangles, 4v6t_withEF-G.pdb_l SES surface, 132714 of 154734 triangles,
4v6t_withEF-G.pdb_n SES surface, 4v6t_withEF-G.pdb_p SES surface,
4v6t_withEF-G.pdb_q SES surface, 29291 of 143310 triangles,
4v6t_withEF-G.pdb_r SES surface, 111572 of 117632 triangles,
4v6t_withEF-G.pdb_s SES surface, 100729 of 110164 triangles,
4v6t_withEF-G.pdb_t SES surface, 1404 of 127746 triangles, 4v6t_withEF-G.pdb_u
SES surface, 4v6t_withEF-G.pdb_v SES surface, 4v6t_withEF-G.pdb_w SES surface,
4v6t_withEF-G.pdb_x SES surface, 4v6t_withEF-G.pdb_y SES surface,
4v6t_withEF-G.pdb_z SES surface, 77716 of 92118 triangles, 4v6t_withEF-G.pdb_0
SES surface, 77245 of 81516 triangles, 4v6t_withEF-G.pdb_1 SES surface,
4v6t_withEF-G.pdb_2 SES surface, 4v6t_withEF-G.pdb_3 SES surface,
4v6t_withEF-G.pdb_Z SES surface, 4v6t_withEF-G.pdb_a SES surface, 44493 of
56210 triangles, 4v6t_withEF-G.pdb_b SES surface, 4v6t_withEF-G.pdb_c SES
surface, 4v6t_withEF-G.pdb_d SES surface, 975 of 44032 triangles,
4v6t_withEF-G.pdb_e SES surface, 210159 of 326338 triangles
Drag select of 4v6t_withEF-G.pdb_f SES surface, 4954088 of 7355268 triangles,
4v6t_withEF-G.pdb_g SES surface, 28204 of 275862 triangles,
4v6t_withEF-G.pdb_h SES surface, 153752 of 207708 triangles,
4v6t_withEF-G.pdb_i SES surface, 4v6t_withEF-G.pdb_k SES surface, 45647 of
168342 triangles, 4v6t_withEF-G.pdb_l SES surface, 143714 of 154734 triangles,
4v6t_withEF-G.pdb_n SES surface, 4v6t_withEF-G.pdb_p SES surface,
4v6t_withEF-G.pdb_q SES surface, 46049 of 143310 triangles,
4v6t_withEF-G.pdb_r SES surface, 115543 of 117632 triangles,
4v6t_withEF-G.pdb_s SES surface, 106390 of 110164 triangles,
4v6t_withEF-G.pdb_t SES surface, 3812 of 127746 triangles, 4v6t_withEF-G.pdb_u
SES surface, 4v6t_withEF-G.pdb_v SES surface, 4v6t_withEF-G.pdb_w SES surface,
4v6t_withEF-G.pdb_x SES surface, 4v6t_withEF-G.pdb_y SES surface,
4v6t_withEF-G.pdb_z SES surface, 85356 of 92118 triangles, 4v6t_withEF-G.pdb_0
SES surface, 79369 of 81516 triangles, 4v6t_withEF-G.pdb_1 SES surface,
4v6t_withEF-G.pdb_2 SES surface, 4v6t_withEF-G.pdb_3 SES surface,
4v6t_withEF-G.pdb_Z SES surface, 4v6t_withEF-G.pdb_a SES surface, 49783 of
56210 triangles, 4v6t_withEF-G.pdb_b SES surface, 4v6t_withEF-G.pdb_c SES
surface, 4v6t_withEF-G.pdb_d SES surface, 3557 of 44032 triangles,
4v6t_withEF-G.pdb_e SES surface, 237478 of 326338 triangles
> select up
291 atoms, 276 bonds, 28 residues, 24 models selected
> select up
66983 atoms, 74765 bonds, 3304 residues, 24 models selected
> select up
85157 atoms, 93206 bonds, 5638 residues, 24 models selected
> select up
85168 atoms, 93217 bonds, 5639 residues, 25 models selected
> select up
85194 atoms, 93243 bonds, 5643 residues, 25 models selected
> select up
86231 atoms, 94299 bonds, 5774 residues, 25 models selected
> select up
86240 atoms, 94307 bonds, 5775 residues, 26 models selected
> select up
86335 atoms, 94402 bonds, 5787 residues, 26 models selected
> select up
86533 atoms, 94602 bonds, 5812 residues, 26 models selected
> select up
86559 atoms, 94625 bonds, 5815 residues, 29 models selected
> select up
86871 atoms, 94943 bonds, 5854 residues, 29 models selected
> select up
89481 atoms, 97586 bonds, 6199 residues, 29 models selected
> select up
89489 atoms, 97593 bonds, 6200 residues, 30 models selected
> select up
89557 atoms, 97661 bonds, 6209 residues, 30 models selected
> select up
90106 atoms, 98221 bonds, 6276 residues, 30 models selected
> select up
90115 atoms, 98229 bonds, 6277 residues, 31 models selected
> select up
90214 atoms, 98328 bonds, 6289 residues, 31 models selected
> select up
90219 atoms, 98332 bonds, 6290 residues, 31 models selected
> select up
90234 atoms, 98347 bonds, 6292 residues, 32 models selected
> select up
90425 atoms, 98541 bonds, 6316 residues, 32 models selected
> select up
90987 atoms, 99114 bonds, 6386 residues, 32 models selected
> color sel dark gray
> select ~sel
671538 atoms, 727966 bonds, 10 pseudobonds, 49950 residues, 11 models selected
> color sel lemon chiffon
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!1 models
> hide #!3 models
Drag select of 4v8q_withEF-Tu.pdb_A SES surface, 4v8q_withEF-Tu.pdb_B SES
surface, 4v8q_withEF-Tu.pdb_C SES surface, 4v8q_withEF-Tu.pdb_D SES surface,
4v8q_withEF-Tu.pdb_E SES surface, 21783 of 62142 triangles, 4v8q_withEF-
Tu.pdb_F SES surface, 4v8q_withEF-Tu.pdb_G SES surface, 4v8q_withEF-Tu.pdb_H
SES surface, 4v8q_withEF-Tu.pdb_I SES surface, 4v8q_withEF-Tu.pdb_J SES
surface, 4v8q_withEF-Tu.pdb_K SES surface, 6866036 of 7461216 triangles,
4v8q_withEF-Tu.pdb_L SES surface, 4v8q_withEF-Tu.pdb_M SES surface, 218194 of
218474 triangles, 4v8q_withEF-Tu.pdb_N SES surface, 274390 of 291894
triangles, 4v8q_withEF-Tu.pdb_O SES surface, 4v8q_withEF-Tu.pdb_P SES surface,
4v8q_withEF-Tu.pdb_Q SES surface, 151824 of 201808 triangles, 4v8q_withEF-
Tu.pdb_R SES surface, 156214 of 178924 triangles, 4v8q_withEF-Tu.pdb_S SES
surface, 57783 of 125096 triangles, 4v8q_withEF-Tu.pdb_U SES surface,
4v8q_withEF-Tu.pdb_V SES surface, 44297 of 110370 triangles, 4v8q_withEF-
Tu.pdb_W SES surface, 4v8q_withEF-Tu.pdb_X SES surface, 151078 of 153360
triangles, 4v8q_withEF-Tu.pdb_Y SES surface, 4v8q_withEF-Tu.pdb_Z SES surface,
4v8q_withEF-Tu.pdb_a SES surface, 91032 of 170520 triangles, 4v8q_withEF-
Tu.pdb_b SES surface, 4v8q_withEF-Tu.pdb_c SES surface, 4v8q_withEF-Tu.pdb_d
SES surface, 4v8q_withEF-Tu.pdb_e SES surface, 4v8q_withEF-Tu.pdb_f SES
surface, 4v8q_withEF-Tu.pdb_g SES surface, 191952 of 207322 triangles,
4v8q_withEF-Tu.pdb_i SES surface, 30632 of 3905368 triangles, 4v8q_withEF-
Tu.pdb_n SES surface, 749 of 110024 triangles, 4v8q_withEF-Tu.pdb_s SES
surface, 3136 of 119518 triangles, 6168 residues
> select up
124672 atoms, 136796 bonds, 8020 residues, 35 models selected
> select down
87466 atoms, 6168 residues, 35 models selected
> select clear
Drag select of 4v8q_withEF-Tu.pdb_A SES surface, 4v8q_withEF-Tu.pdb_B SES
surface, 4v8q_withEF-Tu.pdb_C SES surface, 4v8q_withEF-Tu.pdb_D SES surface,
4v8q_withEF-Tu.pdb_F SES surface, 4v8q_withEF-Tu.pdb_G SES surface, 61089 of
65362 triangles, 4v8q_withEF-Tu.pdb_H SES surface, 4v8q_withEF-Tu.pdb_I SES
surface, 4v8q_withEF-Tu.pdb_J SES surface, 42098 of 45694 triangles,
4v8q_withEF-Tu.pdb_K SES surface, 5852456 of 7461216 triangles, 4v8q_withEF-
Tu.pdb_L SES surface, 301451 of 328776 triangles, 4v8q_withEF-Tu.pdb_M SES
surface, 39964 of 218474 triangles, 4v8q_withEF-Tu.pdb_N SES surface, 61210 of
291894 triangles, 4v8q_withEF-Tu.pdb_O SES surface, 212856 of 213010
triangles, 4v8q_withEF-Tu.pdb_P SES surface, 4v8q_withEF-Tu.pdb_Q SES surface,
1109 of 201808 triangles, 4v8q_withEF-Tu.pdb_R SES surface, 148857 of 178924
triangles, 4v8q_withEF-Tu.pdb_S SES surface, 55135 of 125096 triangles,
4v8q_withEF-Tu.pdb_U SES surface, 4v8q_withEF-Tu.pdb_V SES surface, 20565 of
110370 triangles, 4v8q_withEF-Tu.pdb_W SES surface, 4v8q_withEF-Tu.pdb_X SES
surface, 123932 of 153360 triangles, 4v8q_withEF-Tu.pdb_Y SES surface,
4v8q_withEF-Tu.pdb_Z SES surface, 4v8q_withEF-Tu.pdb_a SES surface, 69103 of
170520 triangles, 4v8q_withEF-Tu.pdb_b SES surface, 4v8q_withEF-Tu.pdb_c SES
surface, 4v8q_withEF-Tu.pdb_d SES surface, 4v8q_withEF-Tu.pdb_e SES surface,
4v8q_withEF-Tu.pdb_f SES surface, 4v8q_withEF-Tu.pdb_g SES surface, 145572 of
207322 triangles, 4v8q_withEF-Tu.pdb_i SES surface, 79 of 3905368 triangles,
5095 residues
> select up
88424 atoms, 96613 bonds, 6012 residues, 31 models selected
> select up
91312 atoms, 99557 bonds, 6407 residues, 31 models selected
> select up
91333 atoms, 99576 bonds, 6410 residues, 33 models selected
> select up
91338 atoms, 99580 bonds, 6411 residues, 33 models selected
> select up
91581 atoms, 99827 bonds, 6448 residues, 33 models selected
> select up
93487 atoms, 101756 bonds, 6728 residues, 33 models selected
> select up
93494 atoms, 101762 bonds, 6729 residues, 34 models selected
> select up
93536 atoms, 101805 bonds, 6734 residues, 34 models selected
> select up
93828 atoms, 102106 bonds, 6773 residues, 34 models selected
> color sel dark gray
> hide #!1 models
> select clear
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!4 models
> select up
7792 atoms, 8715 bonds, 367 residues, 1 model selected
> select up
8968 atoms, 9912 bonds, 514 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!4 surfaces
Drag select of 6q98_P-site.pdb_1 SES surface, 6471944 of 7798404 triangles,
6q98_P-site.pdb_3 SES surface, 6q98_P-site.pdb_6 SES surface, 6q98_P-
site.pdb_B SES surface, 83609 of 303508 triangles, 6q98_P-site.pdb_C SES
surface, 6q98_P-site.pdb_D SES surface, 6q98_P-site.pdb_E SES surface, 141042
of 197708 triangles, 6q98_P-site.pdb_F SES surface, 180827 of 181882
triangles, 6q98_P-site.pdb_G SES surface, 67350 of 169992 triangles, 6q98_P-
site.pdb_H SES surface, 6q98_P-site.pdb_I SES surface, 46034 of 167948
triangles, 6q98_P-site.pdb_J SES surface, 6q98_P-site.pdb_K SES surface, 44931
of 121566 triangles, 6q98_P-site.pdb_L SES surface, 6q98_P-site.pdb_M SES
surface, 6q98_P-site.pdb_N SES surface, 6q98_P-site.pdb_O SES surface, 6q98_P-
site.pdb_P SES surface, 69844 of 134836 triangles, 6q98_P-site.pdb_Q SES
surface, 6q98_P-site.pdb_R SES surface, 6q98_P-site.pdb_S SES surface, 6q98_P-
site.pdb_T SES surface, 6q98_P-site.pdb_U SES surface, 6q98_P-site.pdb_V SES
surface, 6q98_P-site.pdb_W SES surface, 6q98_P-site.pdb_X SES surface, 6q98_P-
site.pdb_Y SES surface, 6q98_P-site.pdb_Z SES surface, 6q98_P-site.pdb_a SES
surface, 28558 of 85390 triangles, 6q98_P-site.pdb_b SES surface, 6q98_P-
site.pdb_c SES surface, 6q98_P-site.pdb_d SES surface, 6q98_P-site.pdb_e SES
surface, 6q98_P-site.pdb_f SES surface, 171 atoms, 5572 residues, 188 bonds,
7701 shapes
> select up
79762 atoms, 86808 bonds, 5613 residues, 35 models selected
> select up
89506 atoms, 97607 bonds, 6193 residues, 35 models selected
> select up
92865 atoms, 100716 bonds, 6898 residues, 35 models selected
> color sel dark gray
> select ~sel
660692 atoms, 716452 bonds, 8 pseudobonds, 48924 residues, 10 models selected
> ~select #1
515375 atoms, 558694 bonds, 8 pseudobonds, 38250 residues, 203 models selected
> ~select #2
370357 atoms, 401729 bonds, 8 pseudobonds, 27270 residues, 148 models selected
> ~select #3
227821 atoms, 246850 bonds, 6 pseudobonds, 16992 residues, 90 models selected
> ~select #5
72652 atoms, 78620 bonds, 6 pseudobonds, 5463 residues, 37 models selected
> ~select #6
63764 atoms, 69108 bonds, 2 pseudobonds, 4717 residues, 35 models selected
> ~select #7
52045 atoms, 56131 bonds, 4073 residues, 27 models selected
> color sel lemon chiffon
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> hide #!4 models
> show #5 models
> show #5 surfaces
> hide #!5 surfaces
> show #!4 models
> hide #!4 models
> select clear
> select #5/4:243
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
7831 atoms, 8754 bonds, 372 residues, 3 models selected
> select up
8698 atoms, 9639 bonds, 481 residues, 3 models selected
> select up
155169 atoms, 168230 bonds, 11529 residues, 3 models selected
> select down
8698 atoms, 9639 bonds, 481 residues, 59 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select clear
> show #!5 surfaces
> hide #!5 cartoons
> hide #!5 cartoons
> hide #!5 atoms
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 6441494 of 7584890
triangles, 6q9a_PastP-site.pdb_2 SES surface, 495 of 4032392 triangles,
6q9a_PastP-site.pdb_3 SES surface, 6q9a_PastP-site.pdb_6 SES surface,
6q9a_PastP-site.pdb_7 SES surface, 136920 of 226010 triangles, 6q9a_PastP-
site.pdb_B SES surface, 104393 of 284462 triangles, 6q9a_PastP-site.pdb_C SES
surface, 209235 of 210654 triangles, 6q9a_PastP-site.pdb_D SES surface,
6q9a_PastP-site.pdb_E SES surface, 173392 of 176940 triangles, 6q9a_PastP-
site.pdb_F SES surface, 167593 of 170510 triangles, 6q9a_PastP-site.pdb_G SES
surface, 90520 of 159078 triangles, 6q9a_PastP-site.pdb_H SES surface,
6q9a_PastP-site.pdb_I SES surface, 34228 of 140114 triangles, 6q9a_PastP-
site.pdb_J SES surface, 6q9a_PastP-site.pdb_K SES surface, 26026 of 118336
triangles, 6q9a_PastP-site.pdb_L SES surface, 6q9a_PastP-site.pdb_M SES
surface, 6q9a_PastP-site.pdb_N SES surface, 6q9a_PastP-site.pdb_O SES surface,
6q9a_PastP-site.pdb_P SES surface, 33058 of 126368 triangles, 6q9a_PastP-
site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES surface, 6q9a_PastP-
site.pdb_S SES surface, 6q9a_PastP-site.pdb_T SES surface, 6q9a_PastP-
site.pdb_U SES surface, 6q9a_PastP-site.pdb_V SES surface, 6q9a_PastP-
site.pdb_W SES surface, 6q9a_PastP-site.pdb_X SES surface, 6q9a_PastP-
site.pdb_Y SES surface, 6q9a_PastP-site.pdb_Z SES surface, 6q9a_PastP-
site.pdb_a SES surface, 60170 of 90478 triangles, 6q9a_PastP-site.pdb_b SES
surface, 6q9a_PastP-site.pdb_c SES surface, 6q9a_PastP-site.pdb_d SES surface,
6q9a_PastP-site.pdb_e SES surface, 6q9a_PastP-site.pdb_f SES surface,
6q9a_PastP-site.pdb_r SES surface, 3895 of 128798 triangles
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 5905425 of 7584890
triangles, 6q9a_PastP-site.pdb_3 SES surface, 336252 of 336264 triangles,
6q9a_PastP-site.pdb_6 SES surface, 6q9a_PastP-site.pdb_7 SES surface, 108606
of 226010 triangles, 6q9a_PastP-site.pdb_B SES surface, 57624 of 284462
triangles, 6q9a_PastP-site.pdb_C SES surface, 202115 of 210654 triangles,
6q9a_PastP-site.pdb_D SES surface, 6q9a_PastP-site.pdb_E SES surface, 149064
of 176940 triangles, 6q9a_PastP-site.pdb_F SES surface, 155194 of 170510
triangles, 6q9a_PastP-site.pdb_G SES surface, 71071 of 159078 triangles,
6q9a_PastP-site.pdb_H SES surface, 149520 of 151294 triangles, 6q9a_PastP-
site.pdb_I SES surface, 9989 of 140114 triangles, 6q9a_PastP-site.pdb_J SES
surface, 6q9a_PastP-site.pdb_K SES surface, 6727 of 118336 triangles,
6q9a_PastP-site.pdb_L SES surface, 6q9a_PastP-site.pdb_M SES surface,
6q9a_PastP-site.pdb_N SES surface, 115431 of 117956 triangles, 6q9a_PastP-
site.pdb_O SES surface, 6q9a_PastP-site.pdb_P SES surface, 19479 of 126368
triangles, 6q9a_PastP-site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES
surface, 6q9a_PastP-site.pdb_S SES surface, 6q9a_PastP-site.pdb_T SES surface,
6q9a_PastP-site.pdb_U SES surface, 6q9a_PastP-site.pdb_V SES surface,
6q9a_PastP-site.pdb_W SES surface, 6q9a_PastP-site.pdb_X SES surface,
6q9a_PastP-site.pdb_Y SES surface, 6q9a_PastP-site.pdb_Z SES surface,
6q9a_PastP-site.pdb_a SES surface, 45322 of 90478 triangles, 6q9a_PastP-
site.pdb_b SES surface, 6q9a_PastP-site.pdb_c SES surface, 6q9a_PastP-
site.pdb_d SES surface, 6q9a_PastP-site.pdb_e SES surface, 6q9a_PastP-
site.pdb_f SES surface
> color sel dark gray
> select ~sel
744859 atoms, 807529 bonds, 10 pseudobonds, 55341 residues, 11 models selected
> ~select #1
599542 atoms, 649771 bonds, 10 pseudobonds, 44667 residues, 294 models
selected
> ~select #2
454524 atoms, 492806 bonds, 10 pseudobonds, 33687 residues, 239 models
selected
> ~select #4
309614 atoms, 335959 bonds, 8 pseudobonds, 22716 residues, 181 models selected
> ~select #3
167078 atoms, 181080 bonds, 6 pseudobonds, 12438 residues, 124 models selected
> ~select #6
158190 atoms, 171568 bonds, 2 pseudobonds, 11692 residues, 70 models selected
> ~select #7
146471 atoms, 158591 bonds, 11048 residues, 62 models selected
> select clear
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 8614 of 7584890 triangles,
6q9a_PastP-site.pdb_2 SES surface, 2994293 of 4032392 triangles, 6q9a_PastP-
site.pdb_7 SES surface, 21762 of 226010 triangles, 6q9a_PastP-site.pdb_a SES
surface, 13295 of 90478 triangles, 6q9a_PastP-site.pdb_g SES surface,
6q9a_PastP-site.pdb_h SES surface, 6q9a_PastP-site.pdb_i SES surface,
6q9a_PastP-site.pdb_j SES surface, 6q9a_PastP-site.pdb_k SES surface, 73366 of
111852 triangles, 6q9a_PastP-site.pdb_l SES surface, 156653 of 158128
triangles, 6q9a_PastP-site.pdb_m SES surface, 6q9a_PastP-site.pdb_n SES
surface, 6q9a_PastP-site.pdb_o SES surface, 6q9a_PastP-site.pdb_p SES surface,
71091 of 118060 triangles, 6q9a_PastP-site.pdb_q SES surface, 112898 of 136950
triangles, 6q9a_PastP-site.pdb_r SES surface, 36411 of 128798 triangles,
6q9a_PastP-site.pdb_s SES surface, 6q9a_PastP-site.pdb_t SES surface, 90024 of
99746 triangles, 6q9a_PastP-site.pdb_u SES surface, 6q9a_PastP-site.pdb_v SES
surface, 83615 of 92440 triangles, 6q9a_PastP-site.pdb_w SES surface, 77805 of
78096 triangles, 6q9a_PastP-site.pdb_x SES surface, 48320 of 94138 triangles,
6q9a_PastP-site.pdb_y SES surface, 4591 of 94832 triangles, 6q9a_PastP-
site.pdb_z SES surface
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 16652 of 7584890 triangles,
6q9a_PastP-site.pdb_2 SES surface, 3114666 of 4032392 triangles, 6q9a_PastP-
site.pdb_7 SES surface, 26718 of 226010 triangles, 6q9a_PastP-site.pdb_a SES
surface, 15549 of 90478 triangles, 6q9a_PastP-site.pdb_g SES surface,
6q9a_PastP-site.pdb_h SES surface, 6q9a_PastP-site.pdb_i SES surface,
6q9a_PastP-site.pdb_j SES surface, 6q9a_PastP-site.pdb_k SES surface, 83802 of
111852 triangles, 6q9a_PastP-site.pdb_l SES surface, 158100 of 158128
triangles, 6q9a_PastP-site.pdb_m SES surface, 6q9a_PastP-site.pdb_n SES
surface, 6q9a_PastP-site.pdb_o SES surface, 6q9a_PastP-site.pdb_p SES surface,
84029 of 118060 triangles, 6q9a_PastP-site.pdb_q SES surface, 117909 of 136950
triangles, 6q9a_PastP-site.pdb_r SES surface, 48588 of 128798 triangles,
6q9a_PastP-site.pdb_s SES surface, 6q9a_PastP-site.pdb_t SES surface, 93982 of
99746 triangles, 6q9a_PastP-site.pdb_u SES surface, 6q9a_PastP-site.pdb_v SES
surface, 87926 of 92440 triangles, 6q9a_PastP-site.pdb_w SES surface,
6q9a_PastP-site.pdb_x SES surface, 56540 of 94138 triangles, 6q9a_PastP-
site.pdb_y SES surface, 9958 of 94832 triangles, 6q9a_PastP-site.pdb_z SES
surface
> select clear
Drag select of 6q9a_PastP-site.pdb_2 SES surface, 679971 of 4032392 triangles,
6q9a_PastP-site.pdb_g SES surface, 120929 of 207704 triangles, 6q9a_PastP-
site.pdb_h SES surface, 197305 of 210806 triangles, 6q9a_PastP-site.pdb_i SES
surface, 191733 of 212800 triangles, 6q9a_PastP-site.pdb_j SES surface, 67187
of 145330 triangles, 6q9a_PastP-site.pdb_m SES surface, 3103 of 123032
triangles, 6q9a_PastP-site.pdb_n SES surface, 49700 of 138712 triangles,
6q9a_PastP-site.pdb_o SES surface, 101443 of 118120 triangles, 6q9a_PastP-
site.pdb_s SES surface, 98585 of 127050 triangles, 6q9a_PastP-site.pdb_u SES
surface, 11155 of 90320 triangles
> select up
186 atoms, 169 bonds, 23 residues, 22 models selected
> select up
34756 atoms, 38695 bonds, 1772 residues, 22 models selected
> select up
52070 atoms, 56158 bonds, 4075 residues, 22 models selected
> color sel lemon chiffon
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
opened ChimeraX session
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!6 models
> open C:/Users/claud/Downloads/4v6t-pdb-bundle.tar/4v6t_withEF-G.pdb
Summary of feedback from opening C:/Users/claud/Downloads/4v6t-pdb-
bundle.tar/4v6t_withEF-G.pdb
---
warning | Ignored bad PDB record found on line 158154
END
Chain information for 4v6t_withEF-G.pdb #8
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
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v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select #6/7:359@CG2
1 atom, 1 residue, 1 model selected
> select #8/V:270@P
1 atom, 1 residue, 1 model selected
> select #6/4:48@O5'
1 atom, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #6
8888 atoms, 9512 bonds, 4 pseudobonds, 746 residues, 2 models selected
> hide #!6 models
> ~select #6
6 models selected
> show #!8 cartoons
> hide #!8 atoms
> show #!6 models
> hide #!6 models
> select #8/X:45
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
8876 atoms, 9911 bonds, 424 residues, 1 model selected
> select up
14983 atoms, 16135 bonds, 1200 residues, 1 model selected
> select ~sel
887395 atoms, 962408 bonds, 12 pseudobonds, 65619 residues, 13 models selected
> ~select #7
875676 atoms, 949431 bonds, 10 pseudobonds, 64975 residues, 295 models
selected
> ~select #6
866788 atoms, 939919 bonds, 6 pseudobonds, 64229 residues, 288 models selected
> ~select #5
720317 atoms, 781328 bonds, 6 pseudobonds, 53181 residues, 281 models selected
> ~select #4
575407 atoms, 624481 bonds, 4 pseudobonds, 42210 residues, 223 models selected
> ~select #3
432871 atoms, 469602 bonds, 2 pseudobonds, 31932 residues, 166 models selected
> select #3
142536 atoms, 154879 bonds, 2 pseudobonds, 10278 residues, 2 models selected
> ~select #2
142536 atoms, 154879 bonds, 2 pseudobonds, 10278 residues, 54 models selected
> ~select #3
52 models selected
> select #8/Y:564
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
41829 atoms, 46814 bonds, 1956 residues, 1 model selected
> select down
75 atoms, 8 bonds, 4 residues, 1 model selected
> select up
41829 atoms, 46814 bonds, 1956 residues, 1 model selected
> select clear
> select up
8875 atoms, 9910 bonds, 424 residues, 1 model selected
> select up
14983 atoms, 16135 bonds, 1200 residues, 1 model selected
> select ~sel
887395 atoms, 962408 bonds, 12 pseudobonds, 65619 residues, 13 models selected
> ~select #7
875676 atoms, 949431 bonds, 10 pseudobonds, 64975 residues, 295 models
selected
> ~select #6
866788 atoms, 939919 bonds, 6 pseudobonds, 64229 residues, 288 models selected
> ~select #5
720317 atoms, 781328 bonds, 6 pseudobonds, 53181 residues, 281 models selected
> ~select #4
575407 atoms, 624481 bonds, 4 pseudobonds, 42210 residues, 223 models selected
> ~select #3
432871 atoms, 469602 bonds, 2 pseudobonds, 31932 residues, 166 models selected
> ~select #2
287853 atoms, 312637 bonds, 2 pseudobonds, 20952 residues, 113 models selected
> ~select #1
142536 atoms, 154879 bonds, 2 pseudobonds, 10278 residues, 56 models selected
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> hide #!8 models
> open C:/Users/claud/Downloads/6q98-pdb-bundle.tar/6q98_P-site.pdb
Summary of feedback from opening C:/Users/claud/Downloads/6q98-pdb-
bundle.tar/6q98_P-site.pdb
---
warning | Ignored bad PDB record found on line 155175
END
Chain information for 6q98_P-site.pdb #9
---
Chain | Description
1 | No description available
2 | No description available
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L | No description available
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Z | No description available
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b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> show #!9 cartoons
> hide #!9 atoms
> select #9/4:272
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
7795 atoms, 8717 bonds, 367 residues, 1 model selected
> select up
8968 atoms, 9912 bonds, 514 residues, 1 model selected
> select ~sel
904752 atoms, 980511 bonds, 16 pseudobonds, 67512 residues, 15 models selected
> ~select #8
889769 atoms, 964376 bonds, 12 pseudobonds, 66312 residues, 297 models
selected
> ~select #7
878050 atoms, 951399 bonds, 10 pseudobonds, 65668 residues, 295 models
selected
> ~select #6
869162 atoms, 941887 bonds, 6 pseudobonds, 64922 residues, 288 models selected
> ~select #5
722691 atoms, 783296 bonds, 6 pseudobonds, 53874 residues, 281 models selected
> ~select #4
577781 atoms, 626449 bonds, 4 pseudobonds, 42903 residues, 223 models selected
> ~select #3
435245 atoms, 471570 bonds, 2 pseudobonds, 32625 residues, 166 models selected
> ~select #2
290227 atoms, 314605 bonds, 2 pseudobonds, 21645 residues, 113 models selected
> ~select #1
144910 atoms, 156847 bonds, 2 pseudobonds, 10971 residues, 56 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> hide #!9 models
> open C:/Users/claud/Downloads/6q9a-pdb-bundle.tar/6q9a_PastP-site.pdb
Summary of feedback from opening C:/Users/claud/Downloads/6q9a-pdb-
bundle.tar/6q9a_PastP-site.pdb
---
warning | Ignored bad PDB record found on line 156504
END
Chain information for 6q9a_PastP-site.pdb #10
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> show #10 cartoons
> hide #10 atoms
> select up
7831 atoms, 8755 bonds, 372 residues, 1 model selected
> select up
8698 atoms, 9639 bonds, 481 residues, 1 model selected
> select ~sel
915281 atoms, 992167 bonds, 14 pseudobonds, 68103 residues, 15 models selected
> ~select #9
906313 atoms, 982255 bonds, 14 pseudobonds, 67589 residues, 298 models
selected
> ~select #8
891330 atoms, 966120 bonds, 10 pseudobonds, 66389 residues, 296 models
selected
> ~select #7
879611 atoms, 953143 bonds, 8 pseudobonds, 65745 residues, 294 models selected
> ~select #6
870723 atoms, 943631 bonds, 4 pseudobonds, 64999 residues, 287 models selected
> ~select #5
724252 atoms, 785040 bonds, 4 pseudobonds, 53951 residues, 280 models selected
> ~select #4
579342 atoms, 628193 bonds, 2 pseudobonds, 42980 residues, 222 models selected
> ~select #3
436806 atoms, 473314 bonds, 32702 residues, 165 models selected
> ~select #2
291788 atoms, 316349 bonds, 21722 residues, 112 models selected
> ~select #1
146471 atoms, 158591 bonds, 11048 residues, 55 models selected
> delete atoms sel
> delete bonds sel
> show #!5 models
> hide #!5 models
> set bgColor white
> set bgColor black
> show #!6 models
> hide #10 models
> show #!8 models
> show #!6,8 surfaces
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!9 models
> show #!6,9 surfaces
> hide #!6 models
> hide #!9 models
> show #10 models
> show #10 surfaces
> show #!9 models
> hide #!10 models
> show #!8 models
> hide #!9 models
> hide #!8 cartoons
> show #!8 cartoons
> show #!6 models
> hide #!8 models
> select #6/5:18@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
104 atoms, 116 bonds, 5 residues, 2 models selected
> color (#!6 & sel) cyan
> select #6/4:44@O4'
1 atom, 1 residue, 1 model selected
> select #6/3:43@N2
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color (#!6 & sel) forest green
> select #6/7:164@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
62 atoms, 64 bonds, 8 residues, 2 models selected
> select up
3015 atoms, 3075 bonds, 381 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sea green
> select #6/6:24@C8
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1305 atoms, 1454 bonds, 62 residues, 2 models selected
> select up
8888 atoms, 9512 bonds, 746 residues, 2 models selected
> select down
1305 atoms, 1454 bonds, 62 residues, 7 models selected
> color sel royal blue
> select #6/h:91@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
112 atoms, 112 bonds, 13 residues, 2 models selected
> select up
1184 atoms, 1203 bonds, 144 residues, 2 models selected
> color sel medium spring green
> color sel medium purple
> select #6/4:44@O3'
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel indian red
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> color sel cadet blue
> color sel blue
> color sel medium violet red
> color sel navy
> color sel medium spring green
> color sel pale green
> color sel light coral
> color sel sky blue
> color sel dark magenta
> color sel magenta
> color sel deep pink
> color sel medium violet red
> color sel dark magenta
> color sel dark orchid
> color sel dark magenta
> color sel medium purple
> color sel purple
> color sel dark magenta
> color sel fire brick
> color sel dark red
> color sel crimson
> color sel brown
> color sel dark magenta
> color sel violet
> color sel aquamarine
> color sel light sky blue
> color sel pale violet red
> color sel salmon
> color sel light salmon
> color sel dark salmon
> color sel pale violet red
> color sel medium violet red
> color sel pale violet red
> color sel midnight blue
> color sel dark slate gray
> color sel dark slate blue
> color sel slate blue
> color sel rebecca purple
> color sel slate blue
> color sel dark magenta
> color sel slate blue
> select clear
> show #!7 models
> hide #!6 models
Drag select of 6q97_A-site.pdb_4 SES surface, 382168 of 1094402 triangles, 123
residues, 2 pseudobonds
> select up
7134 atoms, 7978 bonds, 2 pseudobonds, 334 residues, 3 models selected
> color sel royal blue
> select #7/5:57@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
355 atoms, 360 bonds, 47 residues, 2 models selected
> select up
1170 atoms, 1191 bonds, 145 residues, 2 models selected
> color sel medium purple
> select #7/7:43@C5'
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1644 atoms, 1836 bonds, 77 residues, 2 models selected
> color sel forest green
> select #7/8:44@C4'
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1638 atoms, 1830 bonds, 77 residues, 2 models selected
> select down
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1638 atoms, 1830 bonds, 77 residues, 2 models selected
> color sel slate blue
> select clear
> select #7/9:3@C8
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
128 atoms, 142 bonds, 6 residues, 2 models selected
> color sel cyan
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> hide #!7 models
> show #!8 models
Drag select of 4v6t_withEF-G.pdb_V SES surface, 362955 of 984868 triangles,
122 residues
Drag select of 4v6t_withEF-G.pdb_V SES surface, 394816 of 984868 triangles,
135 residues
> select up
7135 atoms, 7979 bonds, 334 residues, 2 models selected
> color sel royal blue
> select clear
> select #8/W:88@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
78 atoms, 78 bonds, 9 residues, 2 models selected
> select up
993 atoms, 1011 bonds, 122 residues, 2 models selected
> color sel medium purple
> select #8/X:22@O5'
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel slate blue
> select #8/Y:160@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
57 atoms, 56 bonds, 7 residues, 2 models selected
> select up
5215 atoms, 5313 bonds, 667 residues, 2 models selected
> color sel pale violet red
> color sel dark cyan
> color sel teal
> color sel medium aquamarine
> color sel turquoise
> color sel medium turquoise
> color sel medium aquamarine
> select #8/X:9@N1
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
1640 atoms, 1832 bonds, 77 residues, 2 models selected
> color sel forest green
> select clear
> show #!9 models
> hide #!8 models
> show #!10 models
Drag select of 6q98_P-site.pdb_4 SES surface, 190480 of 1142414 triangles,
6q9a_PastP-site.pdb_4 SES surface, 168364 of 1159708 triangles, 123 residues
> select up
15516 atoms, 17362 bonds, 726 residues, 4 models selected
> color sel royal blue
> select clear
> select #9/5:29@CB
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 2 residues, 4 models selected
> select up
409 atoms, 414 bonds, 53 residues, 4 models selected
> select up
2149 atoms, 2189 bonds, 268 residues, 4 models selected
> color sel medium purple
> select clear
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!3 models
Drag select of 4v6t_withEF-G.pdb_l SES surface, 91153 of 154734 triangles,
6q98_P-site.pdb_1 SES surface, 755 of 7798404 triangles, 6q9a_PastP-site.pdb_1
SES surface, 1167 of 7584890 triangles
Drag select of 4v6t_withEF-G.pdb_l SES surface, 81039 of 154734 triangles
> select down
1 model selected
> select down
1 model selected
> select up
141426 atoms, 2 pseudobonds, 10129 residues, 54 models selected
> select down
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
Drag select of 4v6t_withEF-G.pdb_l SES surface, 90513 of 154734 triangles
Drag select of 4v6t_withEF-G.pdb_l SES surface, 91355 of 154734 triangles
> hide #!3 surfaces
> show #!3 surfaces
> surface hidePatches #3.29
> show #!4 models
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!1 models
Drag select of 6q97_A-site.pdb_1 SES surface, 7456581 of 7969538 triangles,
6q97_A-site.pdb_2 SES surface, 11311 of 4256176 triangles, 6q97_A-site.pdb_3
SES surface, 6q97_A-site.pdb_6 SES surface, 6q97_A-site.pdb_B SES surface,
221892 of 295732 triangles, 6q97_A-site.pdb_C SES surface, 6q97_A-site.pdb_D
SES surface, 6q97_A-site.pdb_E SES surface, 167364 of 190010 triangles,
6q97_A-site.pdb_F SES surface, 187344 of 189188 triangles, 6q97_A-site.pdb_G
SES surface, 148494 of 168232 triangles, 6q97_A-site.pdb_H SES surface, 152929
of 153748 triangles, 6q97_A-site.pdb_I SES surface, 13713 of 172054 triangles,
6q97_A-site.pdb_J SES surface, 6q97_A-site.pdb_K SES surface, 64670 of 121150
triangles, 6q97_A-site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface,
6q97_A-site.pdb_N SES surface, 6q97_A-site.pdb_O SES surface, 6q97_A-
site.pdb_P SES surface, 100475 of 137720 triangles, 6q97_A-site.pdb_Q SES
surface, 6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface, 6q97_A-
site.pdb_T SES surface, 6q97_A-site.pdb_U SES surface, 6q97_A-site.pdb_V SES
surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_X SES surface, 6q97_A-
site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface, 6q97_A-site.pdb_a SES
surface, 42705 of 93508 triangles, 6q97_A-site.pdb_b SES surface, 6q97_A-
site.pdb_c SES surface, 6q97_A-site.pdb_d SES surface, 6q97_A-site.pdb_e SES
surface, 6q97_A-site.pdb_f SES surface, 6q97_A-site.pdb_p SES surface, 153 of
123830 triangles
Drag select of 6q97_A-site.pdb_1 SES surface, 6917897 of 7969538 triangles,
6q97_A-site.pdb_2 SES surface, 13172 of 4256176 triangles, 6q97_A-site.pdb_3
SES surface, 6q97_A-site.pdb_6 SES surface, 6q97_A-site.pdb_B SES surface,
196912 of 295732 triangles, 6q97_A-site.pdb_C SES surface, 221995 of 231886
triangles, 6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_E SES surface,
158771 of 190010 triangles, 6q97_A-site.pdb_F SES surface, 127723 of 189188
triangles, 6q97_A-site.pdb_G SES surface, 153800 of 168232 triangles, 6q97_A-
site.pdb_H SES surface, 70038 of 153748 triangles, 6q97_A-site.pdb_J SES
surface, 6q97_A-site.pdb_K SES surface, 7842 of 121150 triangles, 6q97_A-
site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 150944 of 152098
triangles, 6q97_A-site.pdb_N SES surface, 6q97_A-site.pdb_O SES surface,
6q97_A-site.pdb_P SES surface, 20771 of 137720 triangles, 6q97_A-site.pdb_Q
SES surface, 6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface,
6q97_A-site.pdb_T SES surface, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_X SES
surface, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface, 6q97_A-
site.pdb_a SES surface, 40195 of 93508 triangles, 6q97_A-site.pdb_b SES
surface, 6q97_A-site.pdb_c SES surface, 6q97_A-site.pdb_d SES surface, 6q97_A-
site.pdb_e SES surface, 6q97_A-site.pdb_f SES surface, 45830 of 47780
triangles, 6q97_A-site.pdb_p SES surface, 1269 of 123830 triangles
> select clear
> select clear
Drag select of 6q97_A-site.pdb_1 SES surface, 4885059 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 338245 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 30634 of 33600 triangles, 6q97_A-site.pdb_B SES surface, 7903 of
295732 triangles, 6q97_A-site.pdb_C SES surface, 116062 of 231886 triangles,
6q97_A-site.pdb_D SES surface, 135258 of 235976 triangles, 6q97_A-site.pdb_E
SES surface, 3403 of 190010 triangles, 6q97_A-site.pdb_F SES surface, 51153 of
189188 triangles, 6q97_A-site.pdb_G SES surface, 79046 of 168232 triangles,
6q97_A-site.pdb_J SES surface, 6q97_A-site.pdb_L SES surface, 187675 of 188938
triangles, 6q97_A-site.pdb_M SES surface, 58774 of 152098 triangles, 6q97_A-
site.pdb_N SES surface, 75747 of 127082 triangles, 6q97_A-site.pdb_O SES
surface, 6q97_A-site.pdb_Q SES surface, 6q97_A-site.pdb_R SES surface, 122070
of 126390 triangles, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES
surface, 6q97_A-site.pdb_U SES surface, 75593 of 116360 triangles, 6q97_A-
site.pdb_V SES surface, 101270 of 101454 triangles, 6q97_A-site.pdb_W SES
surface, 82378 of 84440 triangles, 6q97_A-site.pdb_X SES surface, 6q97_A-
site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface, 6q97_A-site.pdb_a SES
surface, 3408 of 93508 triangles, 6q97_A-site.pdb_b SES surface, 6q97_A-
site.pdb_c SES surface, 60732 of 63158 triangles, 6q97_A-site.pdb_d SES
surface, 6q97_A-site.pdb_e SES surface, 6q97_A-site.pdb_f SES surface, 1953 of
47780 triangles
> select up
55859 atoms, 4450 residues, 57 models selected
> select down
Nothing selected
Drag select of 6q97_A-site.pdb_1 SES surface, 5495224 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 350080 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 6q97_A-site.pdb_B SES surface, 29299 of 295732 triangles, 6q97_A-
site.pdb_C SES surface, 155702 of 231886 triangles, 6q97_A-site.pdb_D SES
surface, 6q97_A-site.pdb_E SES surface, 33622 of 190010 triangles, 6q97_A-
site.pdb_F SES surface, 73695 of 189188 triangles, 6q97_A-site.pdb_G SES
surface, 97538 of 168232 triangles, 6q97_A-site.pdb_H SES surface, 3185 of
153748 triangles, 6q97_A-site.pdb_J SES surface, 6q97_A-site.pdb_L SES
surface, 6q97_A-site.pdb_M SES surface, 95452 of 152098 triangles, 6q97_A-
site.pdb_N SES surface, 109040 of 127082 triangles, 6q97_A-site.pdb_O SES
surface, 6q97_A-site.pdb_P SES surface, 38 of 137720 triangles, 6q97_A-
site.pdb_Q SES surface, 6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES
surface, 6q97_A-site.pdb_T SES surface, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_X SES
surface, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface, 6q97_A-
site.pdb_a SES surface, 9929 of 93508 triangles, 6q97_A-site.pdb_b SES
surface, 6q97_A-site.pdb_c SES surface, 6q97_A-site.pdb_d SES surface, 6q97_A-
site.pdb_e SES surface, 6q97_A-site.pdb_f SES surface, 10332 of 47780
triangles
Drag select of 6q97_A-site.pdb_1 SES surface, 5094108 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 336907 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 31838 of 33600 triangles, 6q97_A-site.pdb_B SES surface, 11119 of
295732 triangles, 6q97_A-site.pdb_C SES surface, 128627 of 231886 triangles,
6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_E SES surface, 6166 of 190010
triangles, 6q97_A-site.pdb_F SES surface, 57846 of 189188 triangles, 6q97_A-
site.pdb_G SES surface, 83321 of 168232 triangles, 6q97_A-site.pdb_H SES
surface, 23 of 153748 triangles, 6q97_A-site.pdb_J SES surface, 6q97_A-
site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 69065 of 152098
triangles, 6q97_A-site.pdb_N SES surface, 87261 of 127082 triangles, 6q97_A-
site.pdb_O SES surface, 6q97_A-site.pdb_Q SES surface, 6q97_A-site.pdb_R SES
surface, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES surface, 112827
of 112872 triangles, 6q97_A-site.pdb_U SES surface, 6q97_A-site.pdb_V SES
surface, 6q97_A-site.pdb_W SES surface, 83568 of 84440 triangles, 6q97_A-
site.pdb_X SES surface, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES
surface, 6q97_A-site.pdb_a SES surface, 5423 of 93508 triangles, 6q97_A-
site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 62629 of 63158
triangles, 6q97_A-site.pdb_d SES surface, 6q97_A-site.pdb_e SES surface,
6q97_A-site.pdb_f SES surface, 4019 of 47780 triangles
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
67 atoms, 68 bonds, 8 residues, 2 models selected
> select up
984 atoms, 998 bonds, 135 residues, 2 models selected
Drag select of 6q97_A-site.pdb_1 SES surface, 3731009 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 6q97_A-site.pdb_6 SES surface, 10294 of 33600
triangles, 6q97_A-site.pdb_C SES surface, 43178 of 231886 triangles, 6q97_A-
site.pdb_D SES surface, 229647 of 235976 triangles, 6q97_A-site.pdb_E SES
surface, 139012 of 190010 triangles, 6q97_A-site.pdb_F SES surface, 101290 of
189188 triangles, 6q97_A-site.pdb_H SES surface, 136830 of 153748 triangles,
6q97_A-site.pdb_I SES surface, 5064 of 172054 triangles, 6q97_A-site.pdb_J SES
surface, 149752 of 151320 triangles, 6q97_A-site.pdb_L SES surface, 6q97_A-
site.pdb_M SES surface, 133354 of 152098 triangles, 6q97_A-site.pdb_O SES
surface, 6q97_A-site.pdb_Q SES surface, 6q97_A-site.pdb_R SES surface, 6q97_A-
site.pdb_S SES surface, 98853 of 122990 triangles, 6q97_A-site.pdb_T SES
surface, 5887 of 112872 triangles, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_X SES
surface, 2489 of 94844 triangles, 6q97_A-site.pdb_Y SES surface, 26028 of
74596 triangles, 6q97_A-site.pdb_Z SES surface, 6q97_A-site.pdb_a SES surface,
35132 of 93508 triangles, 6q97_A-site.pdb_b SES surface, 45172 of 76920
triangles, 6q97_A-site.pdb_c SES surface, 62373 of 63158 triangles, 6q97_A-
site.pdb_d SES surface, 4840 of 68556 triangles, 6q97_A-site.pdb_e SES
surface, 6q97_A-site.pdb_f SES surface, 33084 of 47780 triangles
Drag select of 6q97_A-site.pdb_1 SES surface, 3193543 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 6q97_A-site.pdb_C SES surface, 88400 of 231886
triangles, 6q97_A-site.pdb_D SES surface, 206092 of 235976 triangles, 6q97_A-
site.pdb_E SES surface, 106039 of 190010 triangles, 6q97_A-site.pdb_F SES
surface, 152053 of 189188 triangles, 6q97_A-site.pdb_H SES surface, 6q97_A-
site.pdb_I SES surface, 60448 of 172054 triangles, 6q97_A-site.pdb_J SES
surface, 6q97_A-site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 135601
of 152098 triangles, 6q97_A-site.pdb_O SES surface, 6q97_A-site.pdb_Q SES
surface, 6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES surface, 87452
of 122990 triangles, 6q97_A-site.pdb_U SES surface, 108820 of 116360
triangles, 6q97_A-site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 81064
of 84440 triangles, 6q97_A-site.pdb_Z SES surface, 6q97_A-site.pdb_a SES
surface, 23935 of 93508 triangles, 6q97_A-site.pdb_b SES surface, 48751 of
76920 triangles, 6q97_A-site.pdb_c SES surface, 32791 of 63158 triangles,
6q97_A-site.pdb_e SES surface, 87953 of 88192 triangles, 6q97_A-site.pdb_f SES
surface, 47342 of 47780 triangles
> select clear
Drag select of 6q97_A-site.pdb_1 SES surface, 5745337 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 347412 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 6q97_A-site.pdb_B SES surface, 11669 of 295732 triangles, 6q97_A-
site.pdb_C SES surface, 231252 of 231886 triangles, 6q97_A-site.pdb_D SES
surface, 6q97_A-site.pdb_E SES surface, 43547 of 190010 triangles, 6q97_A-
site.pdb_F SES surface, 177443 of 189188 triangles, 6q97_A-site.pdb_G SES
surface, 17706 of 168232 triangles, 6q97_A-site.pdb_H SES surface, 149625 of
153748 triangles, 6q97_A-site.pdb_I SES surface, 852 of 172054 triangles,
6q97_A-site.pdb_J SES surface, 6q97_A-site.pdb_K SES surface, 14745 of 121150
triangles, 6q97_A-site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface,
150835 of 152098 triangles, 6q97_A-site.pdb_N SES surface, 6q97_A-site.pdb_O
SES surface, 6q97_A-site.pdb_P SES surface, 36599 of 137720 triangles, 6q97_A-
site.pdb_Q SES surface, 6q97_A-site.pdb_R SES surface, 6q97_A-site.pdb_S SES
surface, 6q97_A-site.pdb_T SES surface, 6q97_A-site.pdb_U SES surface, 6q97_A-
site.pdb_V SES surface, 6q97_A-site.pdb_W SES surface, 6q97_A-site.pdb_X SES
surface, 80746 of 94844 triangles, 6q97_A-site.pdb_Y SES surface, 6q97_A-
site.pdb_Z SES surface, 6q97_A-site.pdb_a SES surface, 4589 of 93508
triangles, 6q97_A-site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 60719
of 63158 triangles, 6q97_A-site.pdb_d SES surface, 6q97_A-site.pdb_e SES
surface, 6q97_A-site.pdb_f SES surface
Drag select of 6q97_A-site.pdb_1 SES surface, 5112671 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 325566 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 33592 of 33600 triangles, 6q97_A-site.pdb_C SES surface, 218667
of 231886 triangles, 6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_E SES
surface, 7764 of 190010 triangles, 6q97_A-site.pdb_F SES surface, 154218 of
189188 triangles, 6q97_A-site.pdb_G SES surface, 2376 of 168232 triangles,
6q97_A-site.pdb_H SES surface, 123307 of 153748 triangles, 6q97_A-site.pdb_J
SES surface, 6q97_A-site.pdb_K SES surface, 151 of 121150 triangles, 6q97_A-
site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 126780 of 152098
triangles, 6q97_A-site.pdb_N SES surface, 124728 of 127082 triangles, 6q97_A-
site.pdb_O SES surface, 6q97_A-site.pdb_P SES surface, 20532 of 137720
triangles, 6q97_A-site.pdb_Q SES surface, 6q97_A-site.pdb_R SES surface,
6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES surface, 6q97_A-
site.pdb_U SES surface, 6q97_A-site.pdb_V SES surface, 6q97_A-site.pdb_W SES
surface, 84108 of 84440 triangles, 6q97_A-site.pdb_X SES surface, 48836 of
94844 triangles, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface,
6q97_A-site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 43501 of 63158
triangles, 6q97_A-site.pdb_d SES surface, 68376 of 68556 triangles, 6q97_A-
site.pdb_e SES surface, 6q97_A-site.pdb_f SES surface, 46169 of 47780
triangles
> select clear
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!2 models
> show #!1 models
> show #!3 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> view
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!8 models
> hide #!6 models
> show #!6 models
> hide #!8 models
> lighting flat
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> set bgColor white
> save C:\Users\claud\Desktop\image1.png supersample 3
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> show #!7 models
> hide #!6 models
> save C:\Users\claud\Desktop\image2.png supersample 3
> show #!8 models
> hide #!7 models
> save C:\Users\claud\Desktop\image3.png supersample 3
> show #!9 models
> hide #!8 models
> save C:\Users\claud\Desktop\image4.png supersample 3
> show #!10 models
> hide #!9 models
> save C:\Users\claud\Desktop\image5.png supersample 3
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!1 models
> show #!6 models
> hide #!6 models
> ui tool show "Side View"
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
opened ChimeraX session
> show #!10 models
> hide #!1 models
> open C:\Users\claud\Downloads\6q9a-pdb-bundle.tar\6q9a_PastP-site.pdb format
> pdb
Summary of feedback from opening C:\Users\claud\Downloads\6q9a-pdb-
bundle.tar\6q9a_PastP-site.pdb
---
warning | Ignored bad PDB record found on line 156504
END
Chain information for 6q9a_PastP-site.pdb #11
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
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r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select #11/7:21@N3
1 atom, 1 residue, 1 model selected
> select clear
> hide #!10 models
> show #!10 models
> hide #!10 models
> select #11/4:188@N1
1 atom, 1 residue, 1 model selected
> select up
51 atoms, 52 bonds, 3 residues, 1 model selected
> select up
9452 atoms, 10564 bonds, 448 residues, 1 model selected
> select up
10323 atoms, 11449 bonds, 561 residues, 1 model selected
> select ~sel
922354 atoms, 999996 bonds, 14 pseudobonds, 68504 residues, 40 models selected
> ~select #10
913656 atoms, 990357 bonds, 14 pseudobonds, 68023 residues, 330 models
selected
> ~select #9
904688 atoms, 980445 bonds, 14 pseudobonds, 67509 residues, 327 models
selected
> ~select #8
889705 atoms, 964310 bonds, 10 pseudobonds, 66309 residues, 323 models
selected
> ~select #7
877986 atoms, 951333 bonds, 8 pseudobonds, 65665 residues, 317 models selected
> ~select #6
869098 atoms, 941821 bonds, 4 pseudobonds, 64919 residues, 310 models selected
> ~select #5
722627 atoms, 783230 bonds, 4 pseudobonds, 53871 residues, 303 models selected
> ~select #4
577717 atoms, 626383 bonds, 2 pseudobonds, 42900 residues, 245 models selected
> ~select #3
435181 atoms, 471504 bonds, 32622 residues, 188 models selected
> ~select #2
290163 atoms, 314539 bonds, 21642 residues, 135 models selected
> ~select #1
144846 atoms, 156781 bonds, 10968 residues, 55 models selected
> delete atoms sel
> delete bonds sel
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #10.1 models
> hide #11 models
> show #10.1 models
> hide #!10.2 models
> show #!10.2 models
> hide #10.2.1 models
> show #10.2.1 models
> hide #10.2.1 models
> show #10.2.1 models
> hide #10.2.1 models
> show #10.2.1 models
> hide #10.1 models
> show #10.1 models
> hide #10.1 models
> show #10.1 models
> close #10
> show #11 models
> hide #11 atoms
> show #11 surfaces
> show #!6 models
> hide #!6 models
> select #11/4:131@C4'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
7758 atoms, 8681 bonds, 363 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel royal blue
> select up
10323 atoms, 11449 bonds, 561 residues, 2 models selected
> select down
7758 atoms, 8681 bonds, 363 residues, 4 models selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel royal blue
> color sel royal blue
> select #11/5:103@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #11/5:103@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
73 atoms, 73 bonds, 9 residues, 2 models selected
> select up
940 atoms, 958 bonds, 118 residues, 2 models selected
> color sel medium purple
> select up
1621 atoms, 76 residues, 3 models selected
> select up
1625 atoms, 1810 bonds, 80 residues, 3 models selected
> select up
1625 atoms, 1810 bonds, 80 residues, 3 models selected
> select up
10323 atoms, 11449 bonds, 561 residues, 3 models selected
> select down
1625 atoms, 1810 bonds, 80 residues, 5 models selected
Drag select of 6q9a_PastP-site.pdb_7 SES surface, 86570 of 226010 triangles,
cap near, 4241 of 6899 triangles
Drag select of 6q9a_PastP-site.pdb_7 SES surface, 111705 of 226010 triangles,
cap near, 5620 of 6899 triangles
> select up
10323 atoms, 11449 bonds, 561 residues, 3 models selected
> select down
1625 atoms, 1810 bonds, 80 residues, 5 models selected
> color sel medium violet red
> color sel dark olive green
> color sel dark magenta
> color sel pale violet red
> select clear
Drag select of 6q9a_PastP-site.pdb_4 SES surface, 175321 of 1159708 triangles,
cap near, 3860 of 9464 triangles
> select up
2561 atoms, 194 residues, 5 models selected
> select down
1 model selected
> color sel royal blue
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl.cxs"
> select clear
> hide #!11 models
> show #!2 models
Drag select of 6q97_A-site.pdb_1 SES surface, 5194422 of 7969538 triangles,
cap near, 25617 of 35589 triangles, 6q97_A-site.pdb_3 SES surface, 8442 of
350468 triangles, cap near, 6q97_A-site.pdb_6 SES surface, 6q97_A-site.pdb_B
SES surface, 44796 of 295732 triangles, 6q97_A-site.pdb_C SES surface, 229471
of 231886 triangles, 6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_F SES
surface, 88137 of 189188 triangles, cap near, 3222 of 4048 triangles, 6q97_A-
site.pdb_G SES surface, 28860 of 168232 triangles, 6q97_A-site.pdb_J SES
surface, 6q97_A-site.pdb_K SES surface, 10835 of 121150 triangles, 6q97_A-
site.pdb_L SES surface, 125520 of 188938 triangles, cap near, 6q97_A-
site.pdb_M SES surface, 35549 of 152098 triangles, cap near, 3719 of 4663
triangles, 6q97_A-site.pdb_N SES surface, 6q97_A-site.pdb_P SES surface, 45549
of 137720 triangles, 6q97_A-site.pdb_Q SES surface, 132694 of 143740
triangles, cap near, 6q97_A-site.pdb_R SES surface, 117339 of 126390
triangles, cap near, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES
surface, 6q97_A-site.pdb_U SES surface, 6q97_A-site.pdb_W SES surface, 7810 of
84440 triangles, cap near, 6q97_A-site.pdb_X SES surface, 6q97_A-site.pdb_Y
SES surface, 6q97_A-site.pdb_Z SES surface, 3047 of 64594 triangles, cap near,
6q97_A-site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 411 of 63158
triangles, cap near, 6q97_A-site.pdb_d SES surface, 6q97_A-site.pdb_e SES
surface, 41006 of 88192 triangles, cap near, 6q97_A-site.pdb_f SES surface,
36052 of 47780 triangles, cap near, 438 of 740 triangles
> select up
57566 atoms, 4665 residues, 69 models selected
> select clear
Drag select of 6q97_A-site.pdb_1 SES surface, 2840895 of 7969538 triangles,
cap near, 15095 of 35589 triangles, 6q97_A-site.pdb_3 SES surface, 4517 of
350468 triangles, cap near, 1423 of 2070 triangles, 6q97_A-site.pdb_6 SES
surface, 20741 of 33600 triangles, 6q97_A-site.pdb_C SES surface, 86112 of
231886 triangles, 6q97_A-site.pdb_D SES surface, 235444 of 235976 triangles,
6q97_A-site.pdb_F SES surface, 7094 of 189188 triangles, cap near, 708 of 4048
triangles, 6q97_A-site.pdb_J SES surface, 144449 of 151320 triangles, 6q97_A-
site.pdb_L SES surface, 123987 of 188938 triangles, cap near, 4629 of 4769
triangles, 6q97_A-site.pdb_N SES surface, 69000 of 127082 triangles, 6q97_A-
site.pdb_Q SES surface, 132694 of 143740 triangles, cap near, 6q97_A-
site.pdb_R SES surface, 117339 of 126390 triangles, cap near, 6q97_A-
site.pdb_S SES surface, 121473 of 122990 triangles, 6q97_A-site.pdb_T SES
surface, 6q97_A-site.pdb_U SES surface, 6q97_A-site.pdb_X SES surface, 1252 of
94844 triangles, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface,
3047 of 64594 triangles, cap near, 6q97_A-site.pdb_b SES surface, 6q97_A-
site.pdb_d SES surface, 45763 of 68556 triangles, 6q97_A-site.pdb_e SES
surface, 38859 of 88192 triangles, cap near, 2322 of 2973 triangles
> select up
64997 atoms, 5622 residues, 65 models selected
> select down
8 models selected
> select down
8 models selected
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!2 models
> ui tool show "Side View"
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!11 models
> show #!6 models
> hide #!11 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> hide #!6 models
> show #!2 models
Drag select of 6q97_A-site.pdb_1 SES surface, 5392686 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 270034 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 33403 of 33600 triangles, 6q97_A-site.pdb_B SES surface, 10826 of
295732 triangles, 6q97_A-site.pdb_C SES surface, 210304 of 231886 triangles,
6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_F SES surface, 103825 of 189188
triangles, 6q97_A-site.pdb_G SES surface, 29150 of 168232 triangles, 6q97_A-
site.pdb_H SES surface, 13463 of 153748 triangles, 6q97_A-site.pdb_J SES
surface, 6q97_A-site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 72913
of 152098 triangles, 6q97_A-site.pdb_N SES surface, 6q97_A-site.pdb_O SES
surface, 119925 of 121204 triangles, 6q97_A-site.pdb_P SES surface, 13996 of
137720 triangles, 6q97_A-site.pdb_Q SES surface, 6q97_A-site.pdb_R SES
surface, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES surface, 6q97_A-
site.pdb_U SES surface, 6q97_A-site.pdb_V SES surface, 6q97_A-site.pdb_W SES
surface, 82105 of 84440 triangles, 6q97_A-site.pdb_X SES surface, 94404 of
94844 triangles, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES surface,
6q97_A-site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 47309 of 63158
triangles, 6q97_A-site.pdb_d SES surface, 6q97_A-site.pdb_e SES surface,
6q97_A-site.pdb_f SES surface, 17333 of 47780 triangles
> select up
55895 atoms, 4449 residues, 57 models selected
> select down
Nothing selected
> hide #2.1 models
> show #2.1 models
> ~select #2.1
Nothing selected
> select #2.2
62336 atoms, 2903 residues, 2 models selected
> select #2.3
32929 atoms, 1534 residues, 2 models selected
> select #2.2
62336 atoms, 2903 residues, 2 models selected
> close #2
> open C:\Users\claud\Downloads\6q97-pdb-bundle.tar\6q97_A-site.pdb format pdb
Summary of feedback from opening C:\Users\claud\Downloads\6q97-pdb-
bundle.tar\6q97_A-site.pdb
---
warning | Ignored bad PDB record found on line 157976
END
Chain information for 6q97_A-site.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
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f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select #2/4:227@O2'
1 atom, 1 residue, 1 model selected
> select clear
> select #2/4:204@P
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 4 residues, 1 model selected
> select up
10771 atoms, 12004 bonds, 535 residues, 1 model selected
> select up
11591 atoms, 12835 bonds, 638 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/6:28@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
140 atoms, 139 bonds, 28 residues, 1 model selected
> select up
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
42 atoms, 46 bonds, 2 residues, 1 model selected
> select up
128 atoms, 142 bonds, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 surfaces
Drag select of 6q97_A-site.pdb_1 SES surface, 5687128 of 7969538 triangles,
6q97_A-site.pdb_3 SES surface, 305764 of 350468 triangles, 6q97_A-site.pdb_6
SES surface, 33398 of 33600 triangles, 6q97_A-site.pdb_B SES surface, 123308
of 295732 triangles, 6q97_A-site.pdb_C SES surface, 115332 of 231886
triangles, 6q97_A-site.pdb_D SES surface, 6q97_A-site.pdb_F SES surface, 11217
of 189188 triangles, 6q97_A-site.pdb_G SES surface, 148479 of 168232
triangles, 6q97_A-site.pdb_J SES surface, 150771 of 151320 triangles, 6q97_A-
site.pdb_L SES surface, 6q97_A-site.pdb_M SES surface, 42789 of 152098
triangles, 6q97_A-site.pdb_N SES surface, 113890 of 127082 triangles, 6q97_A-
site.pdb_O SES surface, 6q97_A-site.pdb_Q SES surface, 6q97_A-site.pdb_R SES
surface, 6q97_A-site.pdb_S SES surface, 6q97_A-site.pdb_T SES surface, 6q97_A-
site.pdb_U SES surface, 6q97_A-site.pdb_V SES surface, 78227 of 101454
triangles, 6q97_A-site.pdb_W SES surface, 83574 of 84440 triangles, 6q97_A-
site.pdb_X SES surface, 6q97_A-site.pdb_Y SES surface, 6q97_A-site.pdb_Z SES
surface, 6q97_A-site.pdb_a SES surface, 4902 of 93508 triangles, 6q97_A-
site.pdb_b SES surface, 6q97_A-site.pdb_c SES surface, 6q97_A-site.pdb_d SES
surface, 6q97_A-site.pdb_e SES surface, 63644 atoms
> select up
66271 atoms, 72006 bonds, 4732 residues, 29 models selected
> select up
84356 atoms, 92158 bonds, 5726 residues, 29 models selected
> hide sel atoms
> select up
87321 atoms, 95095 bonds, 6186 residues, 29 models selected
> select up
144890 atoms, 156823 bonds, 10974 residues, 29 models selected
> select down
87321 atoms, 95095 bonds, 6186 residues, 56 models selected
> select up
87350 atoms, 95121 bonds, 6190 residues, 33 models selected
> select up
87619 atoms, 95396 bonds, 6225 residues, 33 models selected
> select up
91148 atoms, 98970 bonds, 6688 residues, 33 models selected
> select up
144890 atoms, 156823 bonds, 10974 residues, 33 models selected
> select down
91148 atoms, 98970 bonds, 6688 residues, 56 models selected
> select up
91156 atoms, 98977 bonds, 6689 residues, 34 models selected
> select up
91252 atoms, 99073 bonds, 6701 residues, 34 models selected
> select up
91446 atoms, 99268 bonds, 6726 residues, 34 models selected
> color sel dark gray
> select up
91455 atoms, 99276 bonds, 6727 residues, 35 models selected
> select up
91531 atoms, 99355 bonds, 6735 residues, 35 models selected
> select up
92857 atoms, 100703 bonds, 6903 residues, 35 models selected
> color sel dark gray
> select ~sel
686148 atoms, 744180 bonds, 14 pseudobonds, 50707 residues, 66 models selected
> ~select #1
540831 atoms, 586422 bonds, 14 pseudobonds, 40033 residues, 300 models
selected
> ~select #3
398295 atoms, 431543 bonds, 12 pseudobonds, 29755 residues, 244 models
selected
> ~select #4
253385 atoms, 274696 bonds, 10 pseudobonds, 18784 residues, 172 models
selected
> ~select #5
106914 atoms, 116105 bonds, 10 pseudobonds, 7736 residues, 116 models selected
> ~select #6
98026 atoms, 106593 bonds, 6 pseudobonds, 6990 residues, 54 models selected
> ~select #7
86307 atoms, 93616 bonds, 4 pseudobonds, 6346 residues, 42 models selected
> ~select #8
71324 atoms, 77481 bonds, 5146 residues, 35 models selected
> ~select #9
62356 atoms, 67569 bonds, 4632 residues, 30 models selected
> ~select #11
52033 atoms, 56120 bonds, 4071 residues, 25 models selected
> color sel lemon chiffon
> select clear
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting soft
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> hide #!2 models
> open C:\Users\claud\Downloads\6q97-pdb-bundle.tar\6q97_A-site.pdb format pdb
Summary of feedback from opening C:\Users\claud\Downloads\6q97-pdb-
bundle.tar\6q97_A-site.pdb
---
warning | Ignored bad PDB record found on line 157976
END
Chain information for 6q97_A-site.pdb #10
---
Chain | Description
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z | No description available
> show #!10 cartoons
> hide #!10 atoms
> select #10/6:28
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
140 atoms, 139 bonds, 28 residues, 1 model selected
> select up
156609 atoms, 169800 bonds, 11618 residues, 1 model selected
> select down
140 atoms, 139 bonds, 28 residues, 1 model selected
> select ~sel
935474 atoms, 1014544 bonds, 16 pseudobonds, 69200 residues, 68 models
selected
> ~select #1
790157 atoms, 856786 bonds, 16 pseudobonds, 58526 residues, 336 models
selected
> ~select #2
645267 atoms, 699963 bonds, 16 pseudobonds, 47552 residues, 281 models
selected
> ~select #3
502731 atoms, 545084 bonds, 14 pseudobonds, 37274 residues, 224 models
selected
> ~select #4
357821 atoms, 388237 bonds, 12 pseudobonds, 26303 residues, 152 models
selected
> ~select #5
211350 atoms, 229646 bonds, 12 pseudobonds, 15255 residues, 96 models selected
> ~select #6
202462 atoms, 220134 bonds, 8 pseudobonds, 14509 residues, 34 models selected
> ~select #7
190743 atoms, 207157 bonds, 6 pseudobonds, 13865 residues, 22 models selected
> ~select #8
175760 atoms, 191022 bonds, 2 pseudobonds, 12665 residues, 15 models selected
> ~select #9
166792 atoms, 181110 bonds, 2 pseudobonds, 12151 residues, 10 models selected
> ~select #11
156469 atoms, 169661 bonds, 2 pseudobonds, 11590 residues, 5 models selected
> show #!11 models
> hide #!11 models
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> show #!7 models
> hide #!10 models
> show #!10 models
> hide #!7 models
> show #!10 surfaces
> hide #!10 cartoons
> select #10
140 atoms, 139 bonds, 28 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> color sel sandy brown
> color sel maroon
> color sel fire brick
> color sel brown
> color sel dark red
> color sel brown
> color sel crimson
> show #!7 models
> color sel maroon
> color sel fire brick
> color sel peru
> color sel salmon
> color sel indian red
> color sel dark salmon
> color sel salmon
> color sel brown
> color sel steel blue
> color sel cadet blue
> color sel blue
> color sel orange red
> color sel crimson
> color sel dark red
> color sel fire brick
> color sel chocolate
> color sel maroon
> color sel fire brick
> select clear
> hide #!10 models
> hide #!7 models
> open C:\Users\claud\Downloads\4v8q-pdb-bundle.tar\4v8q-pdb-
> bundle\4v8q_withEF-Tu.pdb format pdb
Summary of feedback from opening C:\Users\claud\Downloads\4v8q-pdb-
bundle.tar\4v8q-pdb-bundle\4v8q_withEF-Tu.pdb
---
warning | Ignored bad PDB record found on line 155403
END
Chain information for 4v8q_withEF-Tu.pdb #12
---
Chain | Description
0 | No description available
1 | No description available
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3 4 | No description available
5 | No description available
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z | No description available
> show #!12 cartoons
> hide #!12 atoms
> close #12
> show #!11 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
opened ChimeraX session
> show #!6 models
> hide #!11 models
> lighting flat
> show #!7 models
> show #!8 models
> hide #!7 models
> hide #!6 models
> show #!9 models
> hide #!8 models
> ui tool show "Side View"
> view orient
> set depthCue 0
Expected a keyword
> set depthCue false
Expected a keyword
> set depthCue, false
Expected a keyword
> depthCue false
Unknown command: depthCue false
> lightning
Unknown command: lightning
> lighting
Intensity: 0
Direction: 0.577,-0.577,-0.577
Color: 100,100,100
Fill intensity: 0
Fill direction: -0.2,-0.2,-0.959
Fill color: 100,100,100
Ambient intensity: 1.45
Ambient color: 100,100,100
Depth cue: 1, start 0.5, end 1, color 100,100,100
Shadow: False (depth map size 2048, depth bias 0.005)
Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)
> lighting depthCue false
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!9 models
> select #6/h:91@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
112 atoms, 112 bonds, 13 residues, 2 models selected
> select up
1184 atoms, 1203 bonds, 144 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium violet red
> color sel dark orchid
> color sel dark magenta
> color sel purple
> color sel medium purple
> color sel pale violet red
> color sel medium orchid
> color sel dark violet
> color sel blue violet
> color sel medium orchid
> color sel medium violet red
> select #6/6:56@C4'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
1305 atoms, 1454 bonds, 62 residues, 2 models selected
> color sel cornflower blue
> color sel deep sky blue
> color sel royal blue
> color sel dodger blue
> color sel cornflower blue
> color sel royal blue
> select clear
> hide #!6 models
> show #!7 models
> select #7/5:103@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
34 atoms, 34 bonds, 4 residues, 2 models selected
> select up
1170 atoms, 1191 bonds, 145 residues, 2 models selected
> color sel medium violet red
> select clear
> hide #!7 models
> show #!8 models
> select #8/W:88@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
78 atoms, 78 bonds, 9 residues, 2 models selected
> select up
993 atoms, 1011 bonds, 122 residues, 2 models selected
> color sel medium violet red
> select #8/Y:646@CE1
1 atom, 1 residue, 1 model selected
> select #8/Y:641@CD
1 atom, 1 residue, 1 model selected
> select clear
> select #8/Y:634@SD
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
52 atoms, 52 bonds, 7 residues, 2 models selected
> select up
5215 atoms, 5313 bonds, 667 residues, 2 models selected
> color sel light slate gray
> color sel cadet blue
> color sel steel blue
> color sel cadet blue
> color sel cornflower blue
> color sel cyan
> color sel pale turquoise
> color sel medium turquoise
> color sel turquoise
> color sel medium turquoise
> color sel medium aquamarine
> color sel medium turquoise
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> color sel medium turquoise
> color sel medium aquamarine
> color sel light sea green
> color sel medium aquamarine
> color sel aquamarine
> color sel turquoise
> color sel light sea green
> color sel medium spring green
> color sel teal
> color sel cadet blue
> color sel teal
> color sel aquamarine
> color sel light green
> color sel pale green
> color sel dark sea green
> color sel pale violet red
> color sel thistle
> color sel powder blue
> color sel light steel blue
> color sel sea green
> color sel medium sea green
> color sel fire brick
> color sel dark red
> color sel cornflower blue
> color sel dodger blue
> color sel steel blue
> color sel medium purple
> color sel medium orchid
> color sel blue violet
> color sel slate blue
> color sel dark slate blue
> color sel rebecca purple
> color sel magenta
> color sel deep pink
> color sel pale violet red
> color sel midnight blue
> color sel light coral
> color sel rosy brown
> color sel dark gray
> color sel rosy brown
> color sel gray
> color sel medium aquamarine
> color sel medium turquoise
> color sel medium aquamarine
> color sel turquoise
> color sel medium aquamarine
> color sel aquamarine
> color sel light sea green
> color sel aquamarine
> color sel medium aquamarine
> color sel light sea green
> color sel medium aquamarine
> color sel light sea green
> color sel teal
> color sel medium aquamarine
> color sel dark cyan
> color sel teal
> color sel medium aquamarine
> color sel aquamarine
> color sel medium aquamarine
> color sel plum
> color sel medium aquamarine
> color sel hot pink
> color sel violet
> color sel plum
> color sel light pink
> color sel medium aquamarine
> select clear
> show #!9 models
> hide #!8 models
> select #9/5:28@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
151 atoms, 153 bonds, 18 residues, 2 models selected
> select up
1209 atoms, 1231 bonds, 150 residues, 2 models selected
> color sel medium violet red
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> select clear
> show #!9 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!11 models
> select #11/5:66@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
375 atoms, 380 bonds, 49 residues, 2 models selected
> select up
940 atoms, 958 bonds, 118 residues, 2 models selected
> color sel medium violet red
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> select clear
> set bgColor black
> open C:\Users\claud\Downloads\4v6t-pdb-bundle.tar\4v6t_withEF-G.pdb format
> pdb
Summary of feedback from opening C:\Users\claud\Downloads\4v6t-pdb-
bundle.tar\4v6t_withEF-G.pdb
---
warning | Ignored bad PDB record found on line 158154
END
Chain information for 4v6t_withEF-G.pdb #12
---
Chain | Description
0 | No description available
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> hide #!11 models
> show #!12 cartoons
> hide #!12 atoms
> close #12
> open C:\Users\claud\Downloads\6q98-pdb-bundle.tar\6q98_P-site.pdb format pdb
Summary of feedback from opening C:\Users\claud\Downloads\6q98-pdb-
bundle.tar\6q98_P-site.pdb
---
warning | Ignored bad PDB record found on line 155175
END
Chain information for 6q98_P-site.pdb #12
---
Chain | Description
1 | No description available
2 | No description available
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y | No description available
z | No description available
> show #!12 cartoons
> hide #!12 atoms
> select clear
> select clear
> select clear
Drag select of 19 residues
> select clear
> select #12/6:21
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 8 residues, 1 model selected
> select up
110 atoms, 109 bonds, 22 residues, 1 model selected
> select ~sel
932913 atoms, 1011672 bonds, 16 pseudobonds, 69101 residues, 18 models
selected
> ~select #11
922590 atoms, 1000223 bonds, 16 pseudobonds, 68540 residues, 310 models
selected
> ~select #10
922450 atoms, 1000084 bonds, 16 pseudobonds, 68512 residues, 306 models
selected
> ~select #9
913482 atoms, 990172 bonds, 16 pseudobonds, 67998 residues, 304 models
selected
> ~select #8
898499 atoms, 974037 bonds, 12 pseudobonds, 66798 residues, 300 models
selected
> ~select #7
886780 atoms, 961060 bonds, 10 pseudobonds, 66154 residues, 294 models
selected
> ~select #6
877892 atoms, 951548 bonds, 6 pseudobonds, 65408 residues, 287 models selected
> ~select #5
731421 atoms, 792957 bonds, 6 pseudobonds, 54360 residues, 280 models selected
> ~select #4
586511 atoms, 636110 bonds, 4 pseudobonds, 43389 residues, 222 models selected
> ~select #3
443975 atoms, 481231 bonds, 2 pseudobonds, 33111 residues, 165 models selected
> ~select #2
299085 atoms, 324408 bonds, 2 pseudobonds, 22137 residues, 112 models selected
> ~select #1
153768 atoms, 166650 bonds, 2 pseudobonds, 11463 residues, 56 models selected
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> show #!12 surfaces
> hide #!12 cartoons
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!7 models
> hide #!7 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!12 models
> open C:\Users\claud\Downloads\6q9a-pdb-bundle.tar\6q9a_PastP-site.pdb format
> pdb
Summary of feedback from opening C:\Users\claud\Downloads\6q9a-pdb-
bundle.tar\6q9a_PastP-site.pdb
---
warning | Ignored bad PDB record found on line 156504
END
Chain information for 6q9a_PastP-site.pdb #13
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
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v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> show #13 cartoons
> hide #13 atoms
> select clear
> select #13/6:12
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select up
115 atoms, 114 bonds, 23 residues, 1 model selected
> select ~sel
934309 atoms, 1013247 bonds, 14 pseudobonds, 69166 residues, 18 models
selected
> ~select #1
788992 atoms, 855489 bonds, 14 pseudobonds, 58492 residues, 311 models
selected
> ~select #2
644102 atoms, 698666 bonds, 14 pseudobonds, 47518 residues, 256 models
selected
> ~select #3
501566 atoms, 543787 bonds, 12 pseudobonds, 37240 residues, 199 models
selected
> ~select #4
356656 atoms, 386940 bonds, 10 pseudobonds, 26269 residues, 145 models
selected
> ~select #5
210185 atoms, 228349 bonds, 10 pseudobonds, 15221 residues, 89 models selected
> ~select #6
201297 atoms, 218837 bonds, 6 pseudobonds, 14475 residues, 31 models selected
> ~select #7
189578 atoms, 205860 bonds, 4 pseudobonds, 13831 residues, 23 models selected
> ~select #8
174595 atoms, 189725 bonds, 12631 residues, 16 models selected
> ~select #9
165627 atoms, 179813 bonds, 12117 residues, 11 models selected
> ~select #10
165487 atoms, 179674 bonds, 12089 residues, 8 models selected
> ~select #11
155164 atoms, 168225 bonds, 11528 residues, 6 models selected
> ~select #12
155054 atoms, 168116 bonds, 11506 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> show #13 surfaces
> hide #!13 cartoons
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> hide #!10 models
> show #!5 models
> show #!11 models
> hide #!11 models
> hide #!5 models
> show #!3 models
> show #!8 models
> hide #!3 models
> hide #!8 models
> show #!2 models
> show #!7 models
> hide #!2 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 cartoons
> hide #!8 models
> show #!7 models
> hide #!7 cartoons
> show #!9 models
> hide #!7 models
> show #!11 models
> hide #!9 models
> view name 1
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> set bgColor gray
> set bgColor white
> lighting flat
> lighting soft
> lighting flat
> lighting simple
> lighting flat
> lighting depthCue false
> hide #!11 models
> show #!6 models
> save C:\Users\claud\Desktop\image1.png supersample 3
> hide #!6 models
> show #!7 models
> save C:\Users\claud\Desktop\image2.png supersample 3
> hide #!7 models
> show #!8 models
> show #!8 cartoons
> save C:\Users\claud\Desktop\image3.png supersample 3
> hide #!8 models
> show #!9 models
> save C:\Users\claud\Desktop\image4.png supersample 3
> show #!11 models
> hide #!9 models
> save C:\Users\claud\Desktop\image5.png supersample 3
> hide #!11 models
> show #!1 models
> ui tool show "Side View"
> view name 2
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
——— End of log from Tue Nov 3 01:00:53 2020 ———
opened ChimeraX session
> hide #!1 models
> show #!6 models
> view 1
> select #6/h:18@CD
1 atom, 1 residue, 1 model selected
> select add #6/6:55@C4'
2 atoms, 2 residues, 2 models selected
> select add #6/7:161@CE1
3 atoms, 3 residues, 3 models selected
> select up
41 atoms, 41 bonds, 3 residues, 4 models selected
> select up
1503 atoms, 1653 bonds, 85 residues, 4 models selected
> select up
5504 atoms, 5732 bonds, 587 residues, 4 models selected
> hide sel surfaces
> save C:\Users\claud\Desktop\image1.png supersample 3
> select clear
> hide #!6 models
> show #!5 models
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 5428922 of 7584890
triangles, cap far, 29474 of 36557 triangles, 6q9a_PastP-site.pdb_3 SES
surface, 263333 of 336264 triangles, 6q9a_PastP-site.pdb_6 SES surface,
6q9a_PastP-site.pdb_7 SES surface, 22494 of 226010 triangles, 6q9a_PastP-
site.pdb_B SES surface, 114388 of 284462 triangles, 6q9a_PastP-site.pdb_C SES
surface, 171663 of 210654 triangles, cap far, 7323 of 7385 triangles,
6q9a_PastP-site.pdb_D SES surface, 6q9a_PastP-site.pdb_F SES surface, 114241
of 170510 triangles, 6q9a_PastP-site.pdb_G SES surface, 99083 of 159078
triangles, 6q9a_PastP-site.pdb_H SES surface, 15565 of 151294 triangles,
6q9a_PastP-site.pdb_J SES surface, 6q9a_PastP-site.pdb_K SES surface, 17582 of
118336 triangles, cap far, 575 of 1992 triangles, 6q9a_PastP-site.pdb_L SES
surface, 6q9a_PastP-site.pdb_M SES surface, 95953 of 143600 triangles,
6q9a_PastP-site.pdb_N SES surface, 34054 of 117956 triangles, cap far,
6q9a_PastP-site.pdb_O SES surface, 110407 of 110652 triangles, 6q9a_PastP-
site.pdb_P SES surface, 455 of 126368 triangles, cap far, 229 of 2807
triangles, 6q9a_PastP-site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES
surface, 6q9a_PastP-site.pdb_S SES surface, 6q9a_PastP-site.pdb_T SES surface,
76306 of 106536 triangles, cap far, 6q9a_PastP-site.pdb_U SES surface,
6q9a_PastP-site.pdb_V SES surface, 6q9a_PastP-site.pdb_W SES surface,
6q9a_PastP-site.pdb_X SES surface, 6q9a_PastP-site.pdb_Y SES surface, 71798 of
71820 triangles, cap far, 6q9a_PastP-site.pdb_Z SES surface, 6q9a_PastP-
site.pdb_b SES surface, 48327 of 76322 triangles, cap far, 6q9a_PastP-
site.pdb_c SES surface, 53700 of 58266 triangles, 6q9a_PastP-site.pdb_d SES
surface, 6q9a_PastP-site.pdb_e SES surface, 6q9a_PastP-site.pdb_f SES surface,
27813 of 43520 triangles
> select add #5/I:101@OG
1 atom, 1 residue, 41 models selected
> select clear
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 3540558 of 7584890
triangles, cap far, 14504 of 36557 triangles, 6q9a_PastP-site.pdb_3 SES
surface, 73633 of 336264 triangles, 6q9a_PastP-site.pdb_6 SES surface, 20041
of 27260 triangles, 6q9a_PastP-site.pdb_C SES surface, 88387 of 210654
triangles, cap far, 3455 of 7385 triangles, 6q9a_PastP-site.pdb_D SES surface,
6q9a_PastP-site.pdb_F SES surface, 21126 of 170510 triangles, 6q9a_PastP-
site.pdb_G SES surface, 12726 of 159078 triangles, 6q9a_PastP-site.pdb_J SES
surface, 133212 of 140984 triangles, 6q9a_PastP-site.pdb_L SES surface,
6q9a_PastP-site.pdb_M SES surface, 55 of 143600 triangles, 6q9a_PastP-
site.pdb_N SES surface, 28261 of 117956 triangles, cap far, 3823 of 4257
triangles, 6q9a_PastP-site.pdb_O SES surface, 31759 of 110652 triangles,
6q9a_PastP-site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES surface,
6q9a_PastP-site.pdb_S SES surface, 6q9a_PastP-site.pdb_T SES surface, 76306 of
106536 triangles, cap far, 6q9a_PastP-site.pdb_U SES surface, 6q9a_PastP-
site.pdb_V SES surface, 36442 of 94850 triangles, 6q9a_PastP-site.pdb_W SES
surface, 40639 of 81572 triangles, 6q9a_PastP-site.pdb_X SES surface, 46872 of
88272 triangles, 6q9a_PastP-site.pdb_Y SES surface, 71798 of 71820 triangles,
cap far, 6q9a_PastP-site.pdb_Z SES surface, 6q9a_PastP-site.pdb_b SES surface,
48327 of 76322 triangles, cap far, 6q9a_PastP-site.pdb_c SES surface, 6504 of
58266 triangles, 6q9a_PastP-site.pdb_d SES surface, 58374 of 61184 triangles,
6q9a_PastP-site.pdb_e SES surface, 69733 of 81712 triangles
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 3352002 of 7584890
triangles, cap far, 13089 of 36557 triangles, 6q9a_PastP-site.pdb_3 SES
surface, 52914 of 336264 triangles, 6q9a_PastP-site.pdb_6 SES surface, 18418
of 27260 triangles, 6q9a_PastP-site.pdb_C SES surface, 70699 of 210654
triangles, cap far, 2887 of 7385 triangles, 6q9a_PastP-site.pdb_D SES surface,
6q9a_PastP-site.pdb_F SES surface, 15385 of 170510 triangles, 6q9a_PastP-
site.pdb_G SES surface, 7679 of 159078 triangles, 6q9a_PastP-site.pdb_J SES
surface, 124808 of 140984 triangles, 6q9a_PastP-site.pdb_L SES surface,
6q9a_PastP-site.pdb_N SES surface, 22949 of 117956 triangles, cap far, 3168 of
4257 triangles, 6q9a_PastP-site.pdb_O SES surface, 23823 of 110652 triangles,
6q9a_PastP-site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES surface,
6q9a_PastP-site.pdb_S SES surface, 110512 of 110722 triangles, 6q9a_PastP-
site.pdb_T SES surface, 76306 of 106536 triangles, cap far, 6q9a_PastP-
site.pdb_U SES surface, 6q9a_PastP-site.pdb_V SES surface, 27394 of 94850
triangles, 6q9a_PastP-site.pdb_W SES surface, 33955 of 81572 triangles,
6q9a_PastP-site.pdb_X SES surface, 35351 of 88272 triangles, 6q9a_PastP-
site.pdb_Y SES surface, 71798 of 71820 triangles, cap far, 6q9a_PastP-
site.pdb_Z SES surface, 6q9a_PastP-site.pdb_b SES surface, 48327 of 76322
triangles, cap far, 6q9a_PastP-site.pdb_c SES surface, 3849 of 58266
triangles, 6q9a_PastP-site.pdb_d SES surface, 54729 of 61184 triangles,
6q9a_PastP-site.pdb_e SES surface, 65898 of 81712 triangles
> select clear
Drag select of 6q9a_PastP-site.pdb_2 SES surface, 487961 of 4032392 triangles,
cap far, 208 of 25181 triangles, 6q9a_PastP-site.pdb_g SES surface, 172529 of
207704 triangles, 6q9a_PastP-site.pdb_h SES surface, 183310 of 210806
triangles, 6q9a_PastP-site.pdb_i SES surface, 112004 of 212800 triangles, cap
far, 4339 of 5430 triangles, 6q9a_PastP-site.pdb_j SES surface, 55665 of
145330 triangles, cap far, 715 of 1019 triangles, 6q9a_PastP-site.pdb_m SES
surface, 4979 of 123032 triangles, 6q9a_PastP-site.pdb_n SES surface, 75138 of
138712 triangles, 6q9a_PastP-site.pdb_o SES surface, 99656 of 118120
triangles, 6q9a_PastP-site.pdb_s SES surface, 59610 of 127050 triangles,
6q9a_PastP-site.pdb_z SES surface, 1371 of 108134 triangles
> select clear
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 3682828 of 7584890
triangles, cap far, 15570 of 36557 triangles, 6q9a_PastP-site.pdb_3 SES
surface, 89401 of 336264 triangles, 6q9a_PastP-site.pdb_6 SES surface, 21336
of 27260 triangles, 6q9a_PastP-site.pdb_C SES surface, 100087 of 210654
triangles, cap far, 3903 of 7385 triangles, 6q9a_PastP-site.pdb_D SES surface,
6q9a_PastP-site.pdb_F SES surface, 12300 of 170510 triangles, 6q9a_PastP-
site.pdb_G SES surface, 16863 of 159078 triangles, 6q9a_PastP-site.pdb_J SES
surface, 139516 of 140984 triangles, 6q9a_PastP-site.pdb_L SES surface,
6q9a_PastP-site.pdb_M SES surface, 634 of 143600 triangles, 6q9a_PastP-
site.pdb_N SES surface, 32045 of 117956 triangles, cap far, 4118 of 4257
triangles, 6q9a_PastP-site.pdb_O SES surface, 37139 of 110652 triangles,
6q9a_PastP-site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES surface,
6q9a_PastP-site.pdb_S SES surface, 6q9a_PastP-site.pdb_T SES surface, 76306 of
106536 triangles, cap far, 6q9a_PastP-site.pdb_U SES surface, 6q9a_PastP-
site.pdb_V SES surface, 42572 of 94850 triangles, 6q9a_PastP-site.pdb_W SES
surface, 47304 of 81572 triangles, 6q9a_PastP-site.pdb_X SES surface, 55720 of
88272 triangles, 6q9a_PastP-site.pdb_Y SES surface, 71798 of 71820 triangles,
cap far, 6q9a_PastP-site.pdb_Z SES surface, 6q9a_PastP-site.pdb_b SES surface,
48327 of 76322 triangles, cap far, 6q9a_PastP-site.pdb_c SES surface, 9005 of
58266 triangles, 6q9a_PastP-site.pdb_d SES surface, 59998 of 61184 triangles,
6q9a_PastP-site.pdb_e SES surface, 72252 of 81712 triangles
> select up
61698 atoms, 5075 residues, 63 models selected
> select down
6 models selected
> select clear
> show #!5 cartoons
> hide #!5 cartoons
> ui tool show "Side View"
> view 1
> view 1
> view 2
> view name 2
> hide #!5 models
> show #!1 models
> save C:\Users\claud\Desktop\image1.png supersample 3
> hide #!1 models
> show #!2 models
> save C:\Users\claud\Desktop\image2.png supersample 3
> show #!3 models
> hide #!2 models
> save C:\Users\claud\Desktop\image3.png supersample 3
> show #!4 models
> hide #!3 models
> save C:\Users\claud\Desktop\image4.png supersample 3
> show #!5 models
> hide #!4 models
> save C:\Users\claud\Desktop\image5.png supersample 3
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
> view 1
> view name 1
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
Drag select of 6q9a_PastP-site.pdb_2 SES surface, 734735 of 4032392 triangles,
6q9a_PastP-site.pdb_g SES surface, 193275 of 207704 triangles, 6q9a_PastP-
site.pdb_h SES surface, 202041 of 210806 triangles, 6q9a_PastP-site.pdb_i SES
surface, 185019 of 212800 triangles, 6q9a_PastP-site.pdb_j SES surface, 91758
of 145330 triangles, 6q9a_PastP-site.pdb_l SES surface, 1861 of 158128
triangles, 6q9a_PastP-site.pdb_m SES surface, 30481 of 123032 triangles,
6q9a_PastP-site.pdb_n SES surface, 105345 of 138712 triangles, 6q9a_PastP-
site.pdb_o SES surface, 106532 of 118120 triangles, 6q9a_PastP-site.pdb_s SES
surface, 100102 of 127050 triangles, 6q9a_PastP-site.pdb_u SES surface, 3499
of 90320 triangles, 6q9a_PastP-site.pdb_x SES surface, 278 of 94138 triangles,
6q9a_PastP-site.pdb_z SES surface, 7032 of 108134 triangles
> view 1
> hide #!5 surfaces
> show #!5 surfaces
> view 1
> surface hidePatches #5.37-38,42,44-45,49,54,56#!5.2,39-40,43,51
> select clear
> select #5/r:35@CB
1 atom, 1 residue, 1 model selected
> select add #5/q:86@O
2 atoms, 2 residues, 2 models selected
> select add #5/y:76@CB
3 atoms, 3 residues, 3 models selected
> select add #5/t:31@CD1
4 atoms, 4 residues, 4 models selected
> select add #5/w:12@NH1
5 atoms, 5 residues, 5 models selected
> select add #5/p:98@NH1
6 atoms, 6 residues, 6 models selected
> select up
55 atoms, 49 bonds, 6 residues, 7 models selected
> select up
671 atoms, 671 bonds, 88 residues, 7 models selected
> select up
4636 atoms, 4698 bonds, 592 residues, 7 models selected
> select up
146471 atoms, 158591 bonds, 11048 residues, 7 models selected
> select clear
> select add #5/y:69@CG
1 atom, 1 residue, 1 model selected
> select add #5/v:9@CB
2 atoms, 2 residues, 2 models selected
> select add #5/q:66@CE2
3 atoms, 3 residues, 3 models selected
> select add #5/t:22@OG1
4 atoms, 4 residues, 4 models selected
> select add #5/w:12@CD
5 atoms, 5 residues, 5 models selected
> select add #5/p:98@CG
6 atoms, 6 residues, 6 models selected
> select add #5/r:34@C
7 atoms, 7 residues, 7 models selected
> select up
67 atoms, 61 bonds, 7 residues, 8 models selected
> select up
471 atoms, 467 bonds, 63 residues, 8 models selected
> select up
5285 atoms, 5356 bonds, 672 residues, 8 models selected
> surface hidePatches (#!5 & sel)
> select #5/k:100@O
1 atom, 1 residue, 1 model selected
> select clear
> select #5/k:101@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
89 atoms, 90 bonds, 12 residues, 2 models selected
> select up
848 atoms, 867 bonds, 104 residues, 2 models selected
> surface hidePatches (#!5 & sel)
> view 1
> save C:\Users\claud\Desktop\image6.png supersample 3
> show sel surfaces
> select clear
> select #5
146471 atoms, 158591 bonds, 11048 residues, 18 models selected
> show sel surfaces
> select clear
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 5790145 of 7584890
triangles, 6q9a_PastP-site.pdb_3 SES surface, 236269 of 336264 triangles,
6q9a_PastP-site.pdb_6 SES surface, 6q9a_PastP-site.pdb_7 SES surface, 13731 of
226010 triangles, 6q9a_PastP-site.pdb_B SES surface, 71055 of 284462
triangles, 6q9a_PastP-site.pdb_C SES surface, 206439 of 210654 triangles,
6q9a_PastP-site.pdb_D SES surface, 6q9a_PastP-site.pdb_F SES surface, 101787
of 170510 triangles, 6q9a_PastP-site.pdb_G SES surface, 86146 of 159078
triangles, 6q9a_PastP-site.pdb_H SES surface, 3640 of 151294 triangles,
6q9a_PastP-site.pdb_J SES surface, 6q9a_PastP-site.pdb_K SES surface, 6596 of
118336 triangles, 6q9a_PastP-site.pdb_L SES surface, 6q9a_PastP-site.pdb_M SES
surface, 75188 of 143600 triangles, 6q9a_PastP-site.pdb_N SES surface,
6q9a_PastP-site.pdb_O SES surface, 105561 of 110652 triangles, 6q9a_PastP-
site.pdb_P SES surface, 42160 of 126368 triangles, 6q9a_PastP-site.pdb_Q SES
surface, 6q9a_PastP-site.pdb_R SES surface, 6q9a_PastP-site.pdb_S SES surface,
6q9a_PastP-site.pdb_T SES surface, 6q9a_PastP-site.pdb_U SES surface,
6q9a_PastP-site.pdb_V SES surface, 6q9a_PastP-site.pdb_W SES surface, 80809 of
81572 triangles, 6q9a_PastP-site.pdb_X SES surface, 6q9a_PastP-site.pdb_Y SES
surface, 6q9a_PastP-site.pdb_Z SES surface, 6q9a_PastP-site.pdb_b SES surface,
6q9a_PastP-site.pdb_c SES surface, 47942 of 58266 triangles, 6q9a_PastP-
site.pdb_d SES surface, 6q9a_PastP-site.pdb_e SES surface, 6q9a_PastP-
site.pdb_f SES surface, 20076 of 43520 triangles
Drag select of 6q9a_PastP-site.pdb_1 SES surface, 2104954 of 7584890
triangles, 6q9a_PastP-site.pdb_6 SES surface, 10224 of 27260 triangles,
6q9a_PastP-site.pdb_C SES surface, 8874 of 210654 triangles, 6q9a_PastP-
site.pdb_D SES surface, 185932 of 208968 triangles, 6q9a_PastP-site.pdb_J SES
surface, 76307 of 140984 triangles, 6q9a_PastP-site.pdb_L SES surface, 123816
of 170008 triangles, 6q9a_PastP-site.pdb_N SES surface, 15467 of 117956
triangles, 6q9a_PastP-site.pdb_Q SES surface, 6q9a_PastP-site.pdb_R SES
surface, 111974 of 113126 triangles, 6q9a_PastP-site.pdb_S SES surface, 96913
of 110722 triangles, 6q9a_PastP-site.pdb_T SES surface, 98780 of 106536
triangles, 6q9a_PastP-site.pdb_U SES surface, 6q9a_PastP-site.pdb_W SES
surface, 637 of 81572 triangles, 6q9a_PastP-site.pdb_Y SES surface,
6q9a_PastP-site.pdb_Z SES surface, 48948 of 57718 triangles, 6q9a_PastP-
site.pdb_b SES surface, 67051 of 76322 triangles, 6q9a_PastP-site.pdb_d SES
surface, 11539 of 61184 triangles, 6q9a_PastP-site.pdb_e SES surface, 28367 of
81712 triangles
> select up
70419 atoms, 5989 residues, 57 models selected
> select down
Nothing selected
> select clear
Drag select of 6q9a_PastP-site.pdb_2 SES surface, 626185 of 4032392 triangles,
6q9a_PastP-site.pdb_g SES surface, 185279 of 207704 triangles, 6q9a_PastP-
site.pdb_h SES surface, 195381 of 210806 triangles, 6q9a_PastP-site.pdb_i SES
surface, 164439 of 212800 triangles, 6q9a_PastP-site.pdb_j SES surface, 78469
of 145330 triangles, 6q9a_PastP-site.pdb_l SES surface, 308 of 158128
triangles, 6q9a_PastP-site.pdb_m SES surface, 15294 of 123032 triangles,
6q9a_PastP-site.pdb_n SES surface, 93180 of 138712 triangles, 6q9a_PastP-
site.pdb_o SES surface, 103332 of 118120 triangles, 6q9a_PastP-site.pdb_s SES
surface, 84032 of 127050 triangles, 6q9a_PastP-site.pdb_u SES surface, 1310 of
90320 triangles, 6q9a_PastP-site.pdb_z SES surface, 4320 of 108134 triangles
Drag select of 6q9a_PastP-site.pdb_2 SES surface, 2373397 of 4032392
triangles, 6q9a_PastP-site.pdb_g SES surface, 6q9a_PastP-site.pdb_h SES
surface, 6q9a_PastP-site.pdb_i SES surface, 6q9a_PastP-site.pdb_j SES surface,
6q9a_PastP-site.pdb_l SES surface, 2779 of 158128 triangles, 6q9a_PastP-
site.pdb_m SES surface, 6q9a_PastP-site.pdb_n SES surface, 76579 of 138712
triangles, 6q9a_PastP-site.pdb_o SES surface, 116623 of 118120 triangles,
6q9a_PastP-site.pdb_q SES surface, 85575 of 136950 triangles, 6q9a_PastP-
site.pdb_s SES surface, 106772 of 127050 triangles, 6q9a_PastP-site.pdb_t SES
surface, 12902 of 99746 triangles, 6q9a_PastP-site.pdb_u SES surface,
6q9a_PastP-site.pdb_v SES surface, 62919 of 92440 triangles, 6q9a_PastP-
site.pdb_w SES surface, 281 of 78096 triangles, 6q9a_PastP-site.pdb_x SES
surface, 45 of 94138 triangles, 6q9a_PastP-site.pdb_y SES surface, 37455 of
94832 triangles, 6q9a_PastP-site.pdb_z SES surface, 23079 of 108134 triangles
> select add #5/r:39@CG1
1 atom, 1 residue, 19 models selected
> hide sel surfaces
> show sel surfaces
> select clear
> show #!5 cartoons
> hide #!5 surfaces
> select #5
146471 atoms, 158591 bonds, 11048 residues, 18 models selected
> color sel bychain
> select clear
> show #!5 surfaces
> hide #!5 surfaces
Drag select of 5152 residues
> select up
121592 atoms, 133771 bonds, 7496 residues, 34 models selected
> select down
74666 atoms, 5152 residues, 34 models selected
> select up
121592 atoms, 133771 bonds, 7496 residues, 34 models selected
> select down
74666 atoms, 5152 residues, 34 models selected
> select up
121592 atoms, 133771 bonds, 7496 residues, 34 models selected
> select #5
146471 atoms, 158591 bonds, 11048 residues, 18 models selected
> select clear
> select #5/1:278
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/G:65
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/O:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/W:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/1:2558
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/I:126
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/M:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5/2:223
34 atoms, 36 bonds, 2 residues, 2 models selected
> select add #5/O:84
43 atoms, 44 bonds, 3 residues, 3 models selected
> select add #5/3:8
63 atoms, 65 bonds, 4 residues, 4 models selected
> select add #5/d:21
74 atoms, 75 bonds, 5 residues, 5 models selected
> select add #5/L:83
79 atoms, 79 bonds, 6 residues, 6 models selected
> select add #5/X:72
90 atoms, 89 bonds, 7 residues, 7 models selected
> select add #5/G:45
99 atoms, 97 bonds, 8 residues, 8 models selected
> select add #5/1:364
119 atoms, 118 bonds, 9 residues, 9 models selected
> select add #5/D:103
123 atoms, 121 bonds, 10 residues, 10 models selected
> select add #5/1:1245
146 atoms, 146 bonds, 11 residues, 11 models selected
> select add #5/L:6
154 atoms, 153 bonds, 12 residues, 11 models selected
> select add #5/S:61
162 atoms, 160 bonds, 13 residues, 11 models selected
> select add #5/Q:58
173 atoms, 170 bonds, 14 residues, 12 models selected
> select add #5/V:45
181 atoms, 177 bonds, 15 residues, 13 models selected
> select add #5/I:129
190 atoms, 185 bonds, 16 residues, 14 models selected
> select add #5/F:43
197 atoms, 191 bonds, 17 residues, 15 models selected
> select add #5/Z:36
204 atoms, 197 bonds, 18 residues, 16 models selected
> select add #5/R:24
213 atoms, 205 bonds, 19 residues, 17 models selected
> select add #5/U:71
218 atoms, 209 bonds, 20 residues, 18 models selected
> select add #5/Y:14
226 atoms, 216 bonds, 21 residues, 19 models selected
> select add #5/T:21
232 atoms, 221 bonds, 22 residues, 19 models selected
> select add #5/N:114
241 atoms, 229 bonds, 23 residues, 20 models selected
> select add #5/b:31
249 atoms, 236 bonds, 24 residues, 21 models selected
> select add #5/J:107
253 atoms, 239 bonds, 25 residues, 22 models selected
> select add #5/P:7
262 atoms, 247 bonds, 26 residues, 23 models selected
> select add #5/C:24
269 atoms, 253 bonds, 27 residues, 24 models selected
> select add #5/P:82
277 atoms, 260 bonds, 28 residues, 25 models selected
> select add #5/K:61
284 atoms, 266 bonds, 29 residues, 25 models selected
> select add #5/B:79
293 atoms, 274 bonds, 30 residues, 25 models selected
> select add #5/c:49
305 atoms, 286 bonds, 31 residues, 26 models selected
> select add #5/E:14
314 atoms, 294 bonds, 32 residues, 26 models selected
> select add #5/a:11
323 atoms, 302 bonds, 33 residues, 27 models selected
> select add #5/7:65
345 atoms, 326 bonds, 34 residues, 28 models selected
> select up
102648 atoms, 114564 bonds, 5041 residues, 29 models selected
> select down
345 atoms, 326 bonds, 34 residues, 32 models selected
> select clear
> select #5/1:2398
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69816 bonds, 2903 residues, 2 models selected
> select down
20 atoms, 21 bonds, 1 residue, 2 models selected
> select #5/7:44
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #5/a:13
29 atoms, 30 bonds, 2 residues, 2 models selected
> select add #5/E:96
37 atoms, 37 bonds, 3 residues, 3 models selected
> select add #5/3:35
57 atoms, 58 bonds, 4 residues, 4 models selected
> select add #5/O:74
64 atoms, 64 bonds, 5 residues, 5 models selected
> select add #5/c:36
72 atoms, 71 bonds, 6 residues, 5 models selected
> select add #5/X:57
83 atoms, 81 bonds, 7 residues, 6 models selected
> select add #5/B:172
90 atoms, 87 bonds, 8 residues, 7 models selected
> select add #5/G:51
101 atoms, 97 bonds, 9 residues, 7 models selected
> select add #5/d:33
112 atoms, 107 bonds, 10 residues, 8 models selected
> select add #5/L:133
117 atoms, 111 bonds, 11 residues, 9 models selected
> select add #5/D:106
126 atoms, 119 bonds, 12 residues, 10 models selected
> select add #5/Y:25
135 atoms, 127 bonds, 13 residues, 11 models selected
> select add #5/U:94
146 atoms, 137 bonds, 14 residues, 12 models selected
> select add #5/I:126
157 atoms, 147 bonds, 15 residues, 13 models selected
> select add #5/T:9
166 atoms, 155 bonds, 16 residues, 14 models selected
> select add #5/M:131
173 atoms, 161 bonds, 17 residues, 15 models selected
> select add #5/V:50
181 atoms, 168 bonds, 18 residues, 16 models selected
> select add #5/I:43
186 atoms, 172 bonds, 19 residues, 17 models selected
> select add #5/F:86
195 atoms, 180 bonds, 20 residues, 17 models selected
> select add #5/K:39
203 atoms, 187 bonds, 21 residues, 18 models selected
> select add #5/P:74
214 atoms, 198 bonds, 22 residues, 19 models selected
> select add #5/C:37
221 atoms, 204 bonds, 23 residues, 20 models selected
> select add #5/3:105
244 atoms, 229 bonds, 24 residues, 21 models selected
> select add #5/Z:37
253 atoms, 237 bonds, 25 residues, 21 models selected
> select add #5/R:60
262 atoms, 245 bonds, 26 residues, 22 models selected
> select add #5/S:55
270 atoms, 252 bonds, 27 residues, 23 models selected
> select add #5/1:1445
293 atoms, 277 bonds, 28 residues, 24 models selected
> select add #5/N:87
304 atoms, 288 bonds, 29 residues, 25 models selected
> select add #5/J:31
313 atoms, 296 bonds, 30 residues, 26 models selected
> select add #5/Q:108
318 atoms, 300 bonds, 31 residues, 27 models selected
> select add #5/3:95
338 atoms, 321 bonds, 32 residues, 28 models selected
> select add #5/b:14
342 atoms, 324 bonds, 33 residues, 28 models selected
> select add #5/N:96
353 atoms, 334 bonds, 34 residues, 29 models selected
> select up
69028 atoms, 76994 bonds, 3413 residues, 29 models selected
> select up
91926 atoms, 99931 bonds, 6641 residues, 31 models selected
> select up
146471 atoms, 158591 bonds, 11048 residues, 31 models selected
> select down
91926 atoms, 99931 bonds, 6641 residues, 57 models selected
> hide sel cartoons
> select #5/e:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5/W:69
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add #5/f:16
27 atoms, 25 bonds, 3 residues, 3 models selected
> select add #5/H:16
33 atoms, 30 bonds, 4 residues, 4 models selected
Drag select of 4 residues
> select up
373 atoms, 369 bonds, 57 residues, 6 models selected
> select up
2475 atoms, 2502 bonds, 332 residues, 6 models selected
> hide sel surfaces
> hide sel cartoons
> select clear
Drag select of 3946 residues
> show sel surfaces
> hide sel cartoons
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> view 1
> save C:\Users\claud\Desktop\image7.png supersample 3
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure1_Trans-Transl_v2.cxs"
——— End of log from Fri Nov 6 22:29:56 2020 ———
opened ChimeraX session
> open C:\Users\claud\Downloads\5mgp-pdb-bundle.tar\5mgp-pdb-
> bundle\huter_corrected.pdb format pdb
Summary of feedback from opening C:\Users\claud\Downloads\5mgp-pdb-
bundle.tar\5mgp-pdb-bundle\huter_corrected.pdb
---
warning | Ignored bad PDB record found on line 147218
END
Chain information for huter_corrected.pdb #14
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
z | No description available
> open C:\Users\claud\Downloads\5mdv-pdb-bundle.tar\5mdv-pdb-bundle\5mdv.pdb
> format pdb
Summary of feedback from opening C:\Users\claud\Downloads\5mdv-pdb-
bundle.tar\5mdv-pdb-bundle\5mdv.pdb
---
warning | Ignored bad PDB record found on line 151407
END
Chain information for 5mdv.pdb #15
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide #!14 models
> hide #15 models
> show #15 models
> show #!14 models
> open C:\Users\claud\Downloads\5mdw-pdb-bundle.tar\5mdw-pdb-bundle\5mdw.pdb
> format pdb
Summary of feedback from opening C:\Users\claud\Downloads\5mdw-pdb-
bundle.tar\5mdw-pdb-bundle\5mdw.pdb
---
warning | Ignored bad PDB record found on line 151107
END
Chain information for 5mdw.pdb #16
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> open C:\Users\claud\Downloads\6szs-pdb-bundle.tar\6szs-pdb-bundle\6szs.pdb
> format pdb
Summary of feedback from opening C:\Users\claud\Downloads\6szs-pdb-
bundle.tar\6szs-pdb-bundle\6szs.pdb
---
warning | Ignored bad PDB record found on line 147968
END
Chain information for 6szs.pdb #17
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
x | No description available
y | No description available
z | No description available
> hide #15 models
> hide #!16 models
> hide #17 models
> hide #!5 models
> show #!2 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
——— End of log from Tue Nov 10 00:04:42 2020 ———
opened ChimeraX session
> close #1,3-4,6-10,12
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> ui tool show Matchmaker
> matchmaker #14/A to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with huter_corrected.pdb, chain A
(#14), sequence alignment score = 11493.7
RMSD between 2391 pruned atom pairs is 1.238 angstroms; (across all 2900
pairs: 1.846)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> hide #!14 models
> show #15 models
> ui tool show Matchmaker
> matchmaker #15/1 to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with 5mdv.pdb, chain 1 (#15),
sequence alignment score = 11581.2
RMSD between 2237 pruned atom pairs is 1.314 angstroms; (across all 2903
pairs: 1.819)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> hide #15 models
> show #!16 models
> ui tool show Matchmaker
> matchmaker #16/1 to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with 5mdw.pdb, chain 1 (#16),
sequence alignment score = 11581.2
RMSD between 2323 pruned atom pairs is 1.304 angstroms; (across all 2903
pairs: 1.686)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #17 models
> ui tool show Matchmaker
> matchmaker #17/A to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with 6szs.pdb, chain A (#17),
sequence alignment score = 11514.7
RMSD between 2325 pruned atom pairs is 1.300 angstroms; (across all 2903
pairs: 1.806)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> hide #!2 models
> show #!14 models
> show #15 models
> show #!16 models
> show #15,17#!14,16 surfaces
> hide #!14 models
> hide #!15 models
> hide #!16 models
> select #17/x:20@O2'
1 atom, 1 residue, 1 model selected
> select add #17/z:163@CD
2 atoms, 2 residues, 2 models selected
> select clear
> hide #!17 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!14-17 cartoons
> hide #!14-17 surfaces
> hide #!14-17 atoms
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> select #16/7:72
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #14/z:75
18 atoms, 16 bonds, 2 residues, 3 models selected
> select add #15/7:95
25 atoms, 22 bonds, 3 residues, 5 models selected
> select add #14/z:101
30 atoms, 26 bonds, 4 residues, 6 models selected
> select add #17/z:98
35 atoms, 30 bonds, 5 residues, 7 models selected
> select up
1182 atoms, 1185 bonds, 156 residues, 8 models selected
> select up
11157 atoms, 11316 bonds, 1424 residues, 8 models selected
> delete atoms (#!14-17 & sel)
> delete bonds (#!14-17 & sel)
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!14 models
> show #!14 models
> show #!16 models
> select #17/y:14
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #14/w:16
16 atoms, 14 bonds, 2 residues, 3 models selected
> select add #16/6:16
24 atoms, 21 bonds, 3 residues, 5 models selected
> select add #15/6:20
32 atoms, 28 bonds, 4 residues, 7 models selected
> select up
219 atoms, 217 bonds, 27 residues, 8 models selected
> select up
1441 atoms, 1463 bonds, 177 residues, 8 models selected
> select up
582858 atoms, 632251 bonds, 42935 residues, 8 models selected
> select down
1441 atoms, 1463 bonds, 177 residues, 228 models selected
> delete atoms (#!14-17 & sel)
> delete bonds (#!14-17 & sel)
Drag select of 8 residues
> select up
6536 atoms, 7300 bonds, 306 residues, 8 models selected
> delete atoms (#!14-17 & sel)
> delete bonds (#!14-17 & sel)
> cofr frontCenter
Drag select of 12 residues
> select up
1045 atoms, 1076 bonds, 116 residues, 14 models selected
> select clear
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> show #!17 models
> hide #!14 models
> show #!14 models
> show #!15 models
> show #!16 models
Drag select of 8 residues
> select up
470 atoms, 522 bonds, 22 residues, 8 models selected
> delete atoms (#!14-17 & sel)
> delete bonds (#!14-17 & sel)
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!14-17 surfaces
> hide #!14-17 cartoons
> select clear
Drag select of huter_corrected.pdb_A SES surface, 8300 of 7511814 triangles,
huter_corrected.pdb_T SES surface, 744 of 111618 triangles, 5mdv.pdb_1 SES
surface, 8448 of 7440290 triangles, 5mdv.pdb_T SES surface, 1423 of 106718
triangles, 5mdw.pdb_1 SES surface, 7726 of 7452524 triangles, 5mdw.pdb_T SES
surface, 1265 of 105790 triangles, 6szs.pdb_A SES surface, 7702 of 7397828
triangles, 6szs.pdb_T SES surface, 327 of 100078 triangles
> select clear
Drag select of huter_corrected.pdb_0 SES surface, huter_corrected.pdb_1 SES
surface, 48317 of 59642 triangles, huter_corrected.pdb_2 SES surface,
huter_corrected.pdb_3 SES surface, huter_corrected.pdb_4 SES surface, 29671 of
45510 triangles, huter_corrected.pdb_A SES surface, 5794380 of 7511814
triangles, huter_corrected.pdb_B SES surface, 245661 of 335962 triangles,
huter_corrected.pdb_C SES surface, 65526 of 284254 triangles,
huter_corrected.pdb_D SES surface, 214049 of 215074 triangles,
huter_corrected.pdb_E SES surface, huter_corrected.pdb_G SES surface, 119963
of 176722 triangles, huter_corrected.pdb_H SES surface, 71761 of 160858
triangles, huter_corrected.pdb_J SES surface, huter_corrected.pdb_K SES
surface, 15972 of 116972 triangles, huter_corrected.pdb_L SES surface,
huter_corrected.pdb_M SES surface, 93746 of 146412 triangles,
huter_corrected.pdb_N SES surface, huter_corrected.pdb_O SES surface, 107931
of 111970 triangles, huter_corrected.pdb_P SES surface, 56640 of 128860
triangles, huter_corrected.pdb_Q SES surface, huter_corrected.pdb_R SES
surface, huter_corrected.pdb_S SES surface, huter_corrected.pdb_T SES surface,
huter_corrected.pdb_U SES surface, huter_corrected.pdb_V SES surface,
huter_corrected.pdb_W SES surface, 81346 of 81662 triangles,
huter_corrected.pdb_X SES surface, huter_corrected.pdb_Y SES surface,
huter_corrected.pdb_Z SES surface, 5mdv.pdb_1 SES surface, 5734276 of 7440290
triangles, 5mdv.pdb_3 SES surface, 241363 of 333620 triangles, 5mdv.pdb_B SES
surface, 63341 of 272394 triangles, 5mdv.pdb_C SES surface, 209791 of 210666
triangles, 5mdv.pdb_D SES surface, 5mdv.pdb_F SES surface, 112455 of 163258
triangles, 5mdv.pdb_G SES surface, 70382 of 154882 triangles, 5mdv.pdb_H SES
surface, 18978 of 156914 triangles, 5mdv.pdb_J SES surface, 5mdv.pdb_K SES
surface, 16019 of 111072 triangles, 5mdv.pdb_L SES surface, 5mdv.pdb_M SES
surface, 92101 of 144548 triangles, 5mdv.pdb_N SES surface, 5mdv.pdb_O SES
surface, 104955 of 109580 triangles, 5mdv.pdb_P SES surface, 54443 of 125052
triangles, 5mdv.pdb_Q SES surface, 5mdv.pdb_R SES surface, 5mdv.pdb_S SES
surface, 5mdv.pdb_T SES surface, 5mdv.pdb_U SES surface, 5mdv.pdb_V SES
surface, 5mdv.pdb_W SES surface, 5mdv.pdb_X SES surface, 5mdv.pdb_Y SES
surface, 5mdv.pdb_Z SES surface, 5mdv.pdb_b SES surface, 5mdv.pdb_c SES
surface, 50615 of 60888 triangles, 5mdv.pdb_d SES surface, 5mdv.pdb_e SES
surface, 5mdv.pdb_f SES surface, 29370 of 43268 triangles, 5mdw.pdb_1 SES
surface, 5745894 of 7452524 triangles, 5mdw.pdb_3 SES surface, 242925 of
333528 triangles, 5mdw.pdb_B SES surface, 63406 of 276938 triangles,
5mdw.pdb_C SES surface, 209427 of 210272 triangles, 5mdw.pdb_D SES surface,
5mdw.pdb_F SES surface, 113489 of 166268 triangles, 5mdw.pdb_G SES surface,
71181 of 158460 triangles, 5mdw.pdb_H SES surface, 19963 of 154744 triangles,
5mdw.pdb_J SES surface, 5mdw.pdb_K SES surface, 16021 of 108636 triangles,
5mdw.pdb_L SES surface, 5mdw.pdb_M SES surface, 91699 of 144054 triangles,
5mdw.pdb_N SES surface, 5mdw.pdb_O SES surface, 105899 of 109956 triangles,
5mdw.pdb_P SES surface, 54463 of 123870 triangles, 5mdw.pdb_Q SES surface,
5mdw.pdb_R SES surface, 5mdw.pdb_S SES surface, 5mdw.pdb_T SES surface,
5mdw.pdb_U SES surface, 5mdw.pdb_V SES surface, 5mdw.pdb_W SES surface,
5mdw.pdb_X SES surface, 5mdw.pdb_Y SES surface, 5mdw.pdb_Z SES surface,
5mdw.pdb_b SES surface, 5mdw.pdb_c SES surface, 49482 of 60210 triangles,
5mdw.pdb_d SES surface, 5mdw.pdb_e SES surface, 5mdw.pdb_f SES surface, 29063
of 43246 triangles, 6szs.pdb_0 SES surface, 6szs.pdb_1 SES surface, 45408 of
55612 triangles, 6szs.pdb_2 SES surface, 6szs.pdb_3 SES surface, 6szs.pdb_4
SES surface, 29563 of 43362 triangles, 6szs.pdb_A SES surface, 5717519 of
7397828 triangles, 6szs.pdb_B SES surface, 241899 of 330280 triangles,
6szs.pdb_C SES surface, 64707 of 278468 triangles, 6szs.pdb_D SES surface,
209225 of 210540 triangles, 6szs.pdb_E SES surface, 6szs.pdb_G SES surface,
117964 of 169486 triangles, 6szs.pdb_H SES surface, 71319 of 157824 triangles,
6szs.pdb_J SES surface, 6szs.pdb_K SES surface, 15995 of 110452 triangles,
6szs.pdb_L SES surface, 6szs.pdb_M SES surface, 92265 of 145336 triangles,
6szs.pdb_N SES surface, 6szs.pdb_O SES surface, 107001 of 110850 triangles,
6szs.pdb_P SES surface, 55219 of 126578 triangles, 6szs.pdb_Q SES surface,
6szs.pdb_R SES surface, 6szs.pdb_S SES surface, 6szs.pdb_T SES surface,
6szs.pdb_U SES surface, 6szs.pdb_V SES surface, 6szs.pdb_W SES surface, 79707
of 79960 triangles, 6szs.pdb_X SES surface, 6szs.pdb_Y SES surface, 6szs.pdb_Z
SES surface
> select add #15/I:64@NE
1 atom, 1 residue, 119 models selected
> select up
11 atoms, 10 bonds, 1 residue, 90 models selected
> select clear
Drag select of huter_corrected.pdb_0 SES surface, huter_corrected.pdb_1 SES
surface, 56443 of 59642 triangles, huter_corrected.pdb_2 SES surface,
huter_corrected.pdb_3 SES surface, huter_corrected.pdb_4 SES surface, 25384 of
45510 triangles, huter_corrected.pdb_A SES surface, 6348464 of 7511814
triangles, huter_corrected.pdb_B SES surface, 223360 of 335962 triangles,
huter_corrected.pdb_C SES surface, 202122 of 284254 triangles,
huter_corrected.pdb_D SES surface, huter_corrected.pdb_E SES surface,
huter_corrected.pdb_G SES surface, 111012 of 176722 triangles,
huter_corrected.pdb_H SES surface, 138475 of 160858 triangles,
huter_corrected.pdb_J SES surface, huter_corrected.pdb_K SES surface, 35251 of
116972 triangles, huter_corrected.pdb_L SES surface, huter_corrected.pdb_M SES
surface, 89429 of 146412 triangles, huter_corrected.pdb_N SES surface,
huter_corrected.pdb_O SES surface, 102206 of 111970 triangles,
huter_corrected.pdb_P SES surface, 84631 of 128860 triangles,
huter_corrected.pdb_Q SES surface, huter_corrected.pdb_R SES surface,
huter_corrected.pdb_S SES surface, huter_corrected.pdb_T SES surface,
huter_corrected.pdb_U SES surface, huter_corrected.pdb_V SES surface, 97747 of
99390 triangles, huter_corrected.pdb_W SES surface, huter_corrected.pdb_X SES
surface, huter_corrected.pdb_Y SES surface, huter_corrected.pdb_Z SES surface,
huter_corrected.pdb_a SES surface, 5057 of 4003356 triangles, 5mdv.pdb_1 SES
surface, 6284180 of 7440290 triangles, 5mdv.pdb_2 SES surface, 5186 of 3959882
triangles, 5mdv.pdb_3 SES surface, 219552 of 333620 triangles, 5mdv.pdb_B SES
surface, 195554 of 272394 triangles, 5mdv.pdb_C SES surface, 5mdv.pdb_D SES
surface, 5mdv.pdb_F SES surface, 104397 of 163258 triangles, 5mdv.pdb_G SES
surface, 133797 of 154882 triangles, 5mdv.pdb_H SES surface, 247 of 156914
triangles, 5mdv.pdb_J SES surface, 5mdv.pdb_K SES surface, 34737 of 111072
triangles, 5mdv.pdb_L SES surface, 5mdv.pdb_M SES surface, 88326 of 144548
triangles, 5mdv.pdb_N SES surface, 5mdv.pdb_O SES surface, 99831 of 109580
triangles, 5mdv.pdb_P SES surface, 82412 of 125052 triangles, 5mdv.pdb_Q SES
surface, 5mdv.pdb_R SES surface, 5mdv.pdb_S SES surface, 5mdv.pdb_T SES
surface, 5mdv.pdb_U SES surface, 5mdv.pdb_V SES surface, 91506 of 92456
triangles, 5mdv.pdb_W SES surface, 5mdv.pdb_X SES surface, 5mdv.pdb_Y SES
surface, 5mdv.pdb_Z SES surface, 5mdv.pdb_b SES surface, 5mdv.pdb_c SES
surface, 58005 of 60888 triangles, 5mdv.pdb_d SES surface, 5mdv.pdb_e SES
surface, 5mdv.pdb_f SES surface, 24949 of 43268 triangles, 5mdw.pdb_1 SES
surface, 6294323 of 7452524 triangles, 5mdw.pdb_2 SES surface, 5626 of 3965800
triangles, 5mdw.pdb_3 SES surface, 220828 of 333528 triangles, 5mdw.pdb_B SES
surface, 198314 of 276938 triangles, 5mdw.pdb_C SES surface, 5mdw.pdb_D SES
surface, 5mdw.pdb_F SES surface, 104938 of 166268 triangles, 5mdw.pdb_G SES
surface, 136666 of 158460 triangles, 5mdw.pdb_H SES surface, 480 of 154744
triangles, 5mdw.pdb_J SES surface, 5mdw.pdb_K SES surface, 34424 of 108636
triangles, 5mdw.pdb_L SES surface, 5mdw.pdb_M SES surface, 87562 of 144054
triangles, 5mdw.pdb_N SES surface, 5mdw.pdb_O SES surface, 100725 of 109956
triangles, 5mdw.pdb_P SES surface, 82068 of 123870 triangles, 5mdw.pdb_Q SES
surface, 5mdw.pdb_R SES surface, 5mdw.pdb_S SES surface, 5mdw.pdb_T SES
surface, 5mdw.pdb_U SES surface, 5mdw.pdb_V SES surface, 91561 of 92886
triangles, 5mdw.pdb_W SES surface, 5mdw.pdb_X SES surface, 5mdw.pdb_Y SES
surface, 5mdw.pdb_Z SES surface, 5mdw.pdb_b SES surface, 5mdw.pdb_c SES
surface, 56893 of 60210 triangles, 5mdw.pdb_d SES surface, 5mdw.pdb_e SES
surface, 5mdw.pdb_f SES surface, 24390 of 43246 triangles, 6szs.pdb_0 SES
surface, 6szs.pdb_1 SES surface, 52525 of 55612 triangles, 6szs.pdb_2 SES
surface, 6szs.pdb_3 SES surface, 6szs.pdb_4 SES surface, 25097 of 43362
triangles, 6szs.pdb_A SES surface, 6265361 of 7397828 triangles, 6szs.pdb_B
SES surface, 219594 of 330280 triangles, 6szs.pdb_C SES surface, 198204 of
278468 triangles, 6szs.pdb_D SES surface, 6szs.pdb_E SES surface, 6szs.pdb_G
SES surface, 110125 of 169486 triangles, 6szs.pdb_H SES surface, 138463 of
157824 triangles, 6szs.pdb_J SES surface, 6szs.pdb_K SES surface, 34079 of
110452 triangles, 6szs.pdb_L SES surface, 6szs.pdb_M SES surface, 88272 of
145336 triangles, 6szs.pdb_N SES surface, 6szs.pdb_O SES surface, 101898 of
110850 triangles, 6szs.pdb_P SES surface, 83126 of 126578 triangles,
6szs.pdb_Q SES surface, 6szs.pdb_R SES surface, 6szs.pdb_S SES surface,
6szs.pdb_T SES surface, 6szs.pdb_U SES surface, 6szs.pdb_V SES surface, 92031
of 93086 triangles, 6szs.pdb_W SES surface, 6szs.pdb_X SES surface, 6szs.pdb_Y
SES surface, 6szs.pdb_Z SES surface, 6szs.pdb_a SES surface, 4808 of 3953176
triangles
> select clear
Drag select of huter_corrected.pdb_0 SES surface, huter_corrected.pdb_1 SES
surface, huter_corrected.pdb_2 SES surface, huter_corrected.pdb_3 SES surface,
huter_corrected.pdb_4 SES surface, 42961 of 45510 triangles,
huter_corrected.pdb_6 SES surface, 27172 of 93768 triangles,
huter_corrected.pdb_A SES surface, 6822052 of 7511814 triangles,
huter_corrected.pdb_B SES surface, huter_corrected.pdb_C SES surface, 253284
of 284254 triangles, huter_corrected.pdb_D SES surface, 212533 of 215074
triangles, huter_corrected.pdb_E SES surface, huter_corrected.pdb_F SES
surface, 104052 of 177780 triangles, huter_corrected.pdb_G SES surface, 121459
of 176722 triangles, huter_corrected.pdb_H SES surface, 158572 of 160858
triangles, huter_corrected.pdb_J SES surface, huter_corrected.pdb_K SES
surface, 31084 of 116972 triangles, huter_corrected.pdb_L SES surface,
huter_corrected.pdb_M SES surface, 141095 of 146412 triangles,
huter_corrected.pdb_N SES surface, huter_corrected.pdb_O SES surface,
huter_corrected.pdb_P SES surface, 58590 of 128860 triangles,
huter_corrected.pdb_Q SES surface, huter_corrected.pdb_R SES surface,
huter_corrected.pdb_S SES surface, huter_corrected.pdb_T SES surface,
huter_corrected.pdb_U SES surface, huter_corrected.pdb_V SES surface,
huter_corrected.pdb_W SES surface, huter_corrected.pdb_X SES surface,
huter_corrected.pdb_Y SES surface, huter_corrected.pdb_Z SES surface,
huter_corrected.pdb_a SES surface, 26129 of 4003356 triangles,
huter_corrected.pdb_f SES surface, 735 of 109412 triangles,
huter_corrected.pdb_k SES surface, 3043 of 115294 triangles, 5mdv.pdb_1 SES
surface, 6757878 of 7440290 triangles, 5mdv.pdb_2 SES surface, 26567 of
3959882 triangles, 5mdv.pdb_3 SES surface, 5mdv.pdb_B SES surface, 244000 of
272394 triangles, 5mdv.pdb_C SES surface, 208298 of 210666 triangles,
5mdv.pdb_D SES surface, 5mdv.pdb_E SES surface, 105408 of 174190 triangles,
5mdv.pdb_F SES surface, 113816 of 163258 triangles, 5mdv.pdb_G SES surface,
152842 of 154882 triangles, 5mdv.pdb_H SES surface, 41096 of 156914 triangles,
5mdv.pdb_J SES surface, 5mdv.pdb_K SES surface, 31097 of 111072 triangles,
5mdv.pdb_L SES surface, 5mdv.pdb_M SES surface, 139554 of 144548 triangles,
5mdv.pdb_N SES surface, 5mdv.pdb_O SES surface, 5mdv.pdb_P SES surface, 56243
of 125052 triangles, 5mdv.pdb_Q SES surface, 5mdv.pdb_R SES surface,
5mdv.pdb_S SES surface, 5mdv.pdb_T SES surface, 5mdv.pdb_U SES surface,
5mdv.pdb_V SES surface, 5mdv.pdb_W SES surface, 5mdv.pdb_X SES surface,
5mdv.pdb_Y SES surface, 5mdv.pdb_Z SES surface, 5mdv.pdb_a SES surface, 25686
of 90758 triangles, 5mdv.pdb_b SES surface, 5mdv.pdb_c SES surface, 5mdv.pdb_d
SES surface, 5mdv.pdb_e SES surface, 5mdv.pdb_f SES surface, 40973 of 43268
triangles, 5mdv.pdb_k SES surface, 488 of 107038 triangles, 5mdv.pdb_p SES
surface, 3803 of 119452 triangles, 5mdw.pdb_1 SES surface, 6767482 of 7452524
triangles, 5mdw.pdb_2 SES surface, 25837 of 3965800 triangles, 5mdw.pdb_3 SES
surface, 5mdw.pdb_B SES surface, 247836 of 276938 triangles, 5mdw.pdb_C SES
surface, 207964 of 210272 triangles, 5mdw.pdb_D SES surface, 5mdw.pdb_E SES
surface, 106163 of 174126 triangles, 5mdw.pdb_F SES surface, 114981 of 166268
triangles, 5mdw.pdb_G SES surface, 156335 of 158460 triangles, 5mdw.pdb_H SES
surface, 42800 of 154744 triangles, 5mdw.pdb_J SES surface, 5mdw.pdb_K SES
surface, 30731 of 108636 triangles, 5mdw.pdb_L SES surface, 5mdw.pdb_M SES
surface, 138870 of 144054 triangles, 5mdw.pdb_N SES surface, 5mdw.pdb_O SES
surface, 5mdw.pdb_P SES surface, 56420 of 123870 triangles, 5mdw.pdb_Q SES
surface, 5mdw.pdb_R SES surface, 5mdw.pdb_S SES surface, 5mdw.pdb_T SES
surface, 5mdw.pdb_U SES surface, 5mdw.pdb_V SES surface, 5mdw.pdb_W SES
surface, 5mdw.pdb_X SES surface, 5mdw.pdb_Y SES surface, 5mdw.pdb_Z SES
surface, 5mdw.pdb_a SES surface, 25588 of 91434 triangles, 5mdw.pdb_b SES
surface, 5mdw.pdb_c SES surface, 5mdw.pdb_d SES surface, 5mdw.pdb_e SES
surface, 5mdw.pdb_f SES surface, 40382 of 43246 triangles, 5mdw.pdb_k SES
surface, 316 of 109036 triangles, 5mdw.pdb_p SES surface, 2351 of 119092
triangles, 6szs.pdb_0 SES surface, 6szs.pdb_1 SES surface, 6szs.pdb_2 SES
surface, 6szs.pdb_3 SES surface, 6szs.pdb_4 SES surface, 40799 of 43362
triangles, 6szs.pdb_5 SES surface, 24899 of 89136 triangles, 6szs.pdb_A SES
surface, 6719785 of 7397828 triangles, 6szs.pdb_B SES surface, 6szs.pdb_C SES
surface, 249325 of 278468 triangles, 6szs.pdb_D SES surface, 207861 of 210540
triangles, 6szs.pdb_E SES surface, 6szs.pdb_F SES surface, 102430 of 168170
triangles, 6szs.pdb_G SES surface, 120195 of 169486 triangles, 6szs.pdb_H SES
surface, 156380 of 157824 triangles, 6szs.pdb_J SES surface, 6szs.pdb_K SES
surface, 30360 of 110452 triangles, 6szs.pdb_L SES surface, 6szs.pdb_M SES
surface, 141214 of 145336 triangles, 6szs.pdb_N SES surface, 6szs.pdb_O SES
surface, 6szs.pdb_P SES surface, 56820 of 126578 triangles, 6szs.pdb_Q SES
surface, 6szs.pdb_R SES surface, 6szs.pdb_S SES surface, 6szs.pdb_T SES
surface, 6szs.pdb_U SES surface, 6szs.pdb_V SES surface, 6szs.pdb_W SES
surface, 6szs.pdb_X SES surface, 6szs.pdb_Y SES surface, 6szs.pdb_Z SES
surface, 6szs.pdb_a SES surface, 27874 of 3953176 triangles, 6szs.pdb_f SES
surface, 665 of 100246 triangles, 6szs.pdb_k SES surface, 3596 of 115982
triangles
> color
> #14.2-33,38,43#15.1-3,8-14,16-38,43,48#16.2-4,9-15,17-39,44,49#17.1-32,37,42
> dark gray
> select clear
> select #16/I:44@CA
1 atom, 1 residue, 1 model selected
Drag select of huter_corrected.pdb_A SES surface, 44897 of 7511814 triangles,
huter_corrected.pdb_C SES surface, 5725 of 284254 triangles,
huter_corrected.pdb_H SES surface, 10182 of 160858 triangles,
huter_corrected.pdb_X SES surface, 10537 of 91202 triangles, 5mdv.pdb_1 SES
surface, 47044 of 7440290 triangles, 5mdv.pdb_B SES surface, 5535 of 272394
triangles, 5mdv.pdb_G SES surface, 9715 of 154882 triangles, 5mdv.pdb_I SES
surface, 13443 of 150166 triangles, 5mdv.pdb_X SES surface, 10773 of 87410
triangles, 5mdw.pdb_1 SES surface, 47371 of 7452524 triangles, 5mdw.pdb_B SES
surface, 5835 of 276938 triangles, 5mdw.pdb_G SES surface, 9748 of 158460
triangles, 5mdw.pdb_I SES surface, 12302 of 155174 triangles, 5mdw.pdb_X SES
surface, 11012 of 87482 triangles, 6szs.pdb_A SES surface, 47846 of 7397828
triangles, 6szs.pdb_C SES surface, 5460 of 278468 triangles, 6szs.pdb_H SES
surface, 10126 of 157824 triangles, 6szs.pdb_X SES surface, 9870 of 88422
triangles
> select clear
Drag select of huter_corrected.pdb_A SES surface, 28903 of 7511814 triangles,
huter_corrected.pdb_C SES surface, 395 of 284254 triangles,
huter_corrected.pdb_H SES surface, 10201 of 160858 triangles,
huter_corrected.pdb_X SES surface, 2071 of 91202 triangles, 5mdv.pdb_1 SES
surface, 28845 of 7440290 triangles, 5mdv.pdb_B SES surface, 341 of 272394
triangles, 5mdv.pdb_G SES surface, 10295 of 154882 triangles, 5mdv.pdb_I SES
surface, 6488 of 150166 triangles, 5mdv.pdb_X SES surface, 1880 of 87410
triangles, 5mdw.pdb_1 SES surface, 28654 of 7452524 triangles, 5mdw.pdb_B SES
surface, 395 of 276938 triangles, 5mdw.pdb_G SES surface, 10251 of 158460
triangles, 5mdw.pdb_I SES surface, 6574 of 155174 triangles, 5mdw.pdb_X SES
surface, 1986 of 87482 triangles, 6szs.pdb_A SES surface, 28829 of 7397828
triangles, 6szs.pdb_C SES surface, 277 of 278468 triangles, 6szs.pdb_H SES
surface, 10853 of 157824 triangles, 6szs.pdb_X SES surface, 1601 of 88422
triangles
> select clear
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> show #!15 models
Drag select of 5mdv.pdb_1 SES surface, 20481 of 7440290 triangles, 5mdv.pdb_B
SES surface, 170 of 272394 triangles, 5mdv.pdb_G SES surface, 5999 of 154882
triangles, 5mdv.pdb_I SES surface, 6469 of 150166 triangles, 5mdv.pdb_X SES
surface, 6875 of 87410 triangles, 5mdw.pdb_1 SES surface, 20209 of 7452524
triangles, 5mdw.pdb_B SES surface, 175 of 276938 triangles, 5mdw.pdb_G SES
surface, 5923 of 158460 triangles, 5mdw.pdb_I SES surface, 6228 of 155174
triangles, 5mdw.pdb_X SES surface, 6904 of 87482 triangles
> select clear
> hide #!16 models
> select #15/I:44@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
110 atoms, 111 bonds, 14 residues, 2 models selected
> select up
984 atoms, 998 bonds, 135 residues, 2 models selected
> color (#!15 & sel) dark gray
> select clear
> show #!16 models
> hide #!15 models
> select #16/I:68@CE1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
211 atoms, 217 bonds, 27 residues, 2 models selected
> select up
984 atoms, 998 bonds, 135 residues, 2 models selected
> color (#!16 & sel) dark gray
> select clear
> show #!17 models
> show #!15 models
> show #!14 models
Drag select of huter_corrected.pdb_6 SES surface, 14326 of 93768 triangles,
huter_corrected.pdb_A SES surface, 152118 of 7511814 triangles,
huter_corrected.pdb_C SES surface, 819 of 284254 triangles,
huter_corrected.pdb_H SES surface, 23978 of 160858 triangles,
huter_corrected.pdb_a SES surface, 2780682 of 4003356 triangles,
huter_corrected.pdb_b SES surface, huter_corrected.pdb_c SES surface,
huter_corrected.pdb_d SES surface, huter_corrected.pdb_e SES surface,
huter_corrected.pdb_f SES surface, 109411 of 109412 triangles,
huter_corrected.pdb_g SES surface, huter_corrected.pdb_h SES surface,
huter_corrected.pdb_i SES surface, huter_corrected.pdb_j SES surface,
huter_corrected.pdb_k SES surface, huter_corrected.pdb_l SES surface, 86219 of
141304 triangles, huter_corrected.pdb_m SES surface, 67002 of 126116
triangles, huter_corrected.pdb_n SES surface, huter_corrected.pdb_o SES
surface, 100753 of 102000 triangles, huter_corrected.pdb_p SES surface, 84675
of 87966 triangles, huter_corrected.pdb_q SES surface, 69176 of 92162
triangles, huter_corrected.pdb_r SES surface, huter_corrected.pdb_s SES
surface, 44202 of 96886 triangles, huter_corrected.pdb_u SES surface,
5mdv.pdb_1 SES surface, 146360 of 7440290 triangles, 5mdv.pdb_2 SES surface,
2741474 of 3959882 triangles, 5mdv.pdb_B SES surface, 390 of 272394 triangles,
5mdv.pdb_G SES surface, 22958 of 154882 triangles, 5mdv.pdb_a SES surface,
13786 of 90758 triangles, 5mdv.pdb_g SES surface, 5mdv.pdb_h SES surface,
5mdv.pdb_i SES surface, 5mdv.pdb_j SES surface, 5mdv.pdb_k SES surface, 106852
of 107038 triangles, 5mdv.pdb_l SES surface, 5mdv.pdb_m SES surface,
5mdv.pdb_n SES surface, 5mdv.pdb_o SES surface, 5mdv.pdb_p SES surface,
5mdv.pdb_q SES surface, 82902 of 133776 triangles, 5mdv.pdb_r SES surface,
62477 of 124820 triangles, 5mdv.pdb_s SES surface, 5mdv.pdb_t SES surface,
95949 of 97168 triangles, 5mdv.pdb_u SES surface, 82709 of 85776 triangles,
5mdv.pdb_v SES surface, 71348 of 93224 triangles, 5mdv.pdb_w SES surface,
5mdv.pdb_x SES surface, 42483 of 94056 triangles, 5mdv.pdb_z SES surface,
5mdw.pdb_1 SES surface, 147261 of 7452524 triangles, 5mdw.pdb_2 SES surface,
2747061 of 3965800 triangles, 5mdw.pdb_B SES surface, 476 of 276938 triangles,
5mdw.pdb_G SES surface, 23360 of 158460 triangles, 5mdw.pdb_a SES surface,
14095 of 91434 triangles, 5mdw.pdb_g SES surface, 5mdw.pdb_h SES surface,
5mdw.pdb_i SES surface, 5mdw.pdb_j SES surface, 5mdw.pdb_k SES surface, 108913
of 109036 triangles, 5mdw.pdb_l SES surface, 5mdw.pdb_m SES surface,
5mdw.pdb_n SES surface, 5mdw.pdb_o SES surface, 5mdw.pdb_p SES surface,
5mdw.pdb_q SES surface, 81907 of 133904 triangles, 5mdw.pdb_r SES surface,
62034 of 125246 triangles, 5mdw.pdb_s SES surface, 5mdw.pdb_t SES surface,
95483 of 96506 triangles, 5mdw.pdb_u SES surface, 83108 of 86502 triangles,
5mdw.pdb_v SES surface, 70571 of 92660 triangles, 5mdw.pdb_w SES surface,
5mdw.pdb_x SES surface, 39146 of 92976 triangles, 5mdw.pdb_z SES surface,
6szs.pdb_5 SES surface, 12877 of 89136 triangles, 6szs.pdb_A SES surface,
133699 of 7397828 triangles, 6szs.pdb_C SES surface, 455 of 278468 triangles,
6szs.pdb_H SES surface, 21567 of 157824 triangles, 6szs.pdb_a SES surface,
2752479 of 3953176 triangles, 6szs.pdb_b SES surface, 6szs.pdb_c SES surface,
6szs.pdb_d SES surface, 6szs.pdb_e SES surface, 6szs.pdb_f SES surface, 100020
of 100246 triangles, 6szs.pdb_g SES surface, 6szs.pdb_h SES surface,
6szs.pdb_i SES surface, 6szs.pdb_j SES surface, 6szs.pdb_k SES surface, 115944
of 115982 triangles, 6szs.pdb_l SES surface, 84200 of 134408 triangles,
6szs.pdb_m SES surface, 61383 of 120740 triangles, 6szs.pdb_n SES surface,
6szs.pdb_o SES surface, 93852 of 95042 triangles, 6szs.pdb_p SES surface,
85274 of 88464 triangles, 6szs.pdb_q SES surface, 67340 of 89452 triangles,
6szs.pdb_r SES surface, 6szs.pdb_s SES surface, 43946 of 93284 triangles,
6szs.pdb_u SES surface
> select clear
Drag select of huter_corrected.pdb_A SES surface, 46 of 7511814 triangles,
huter_corrected.pdb_a SES surface, 1370282 of 4003356 triangles,
huter_corrected.pdb_b SES surface, huter_corrected.pdb_c SES surface, 208185
of 209098 triangles, huter_corrected.pdb_d SES surface, 206388 of 209444
triangles, huter_corrected.pdb_e SES surface, huter_corrected.pdb_f SES
surface, 22307 of 109412 triangles, huter_corrected.pdb_g SES surface, 89037
of 158486 triangles, huter_corrected.pdb_h SES surface, 123843 of 123984
triangles, huter_corrected.pdb_i SES surface, 131541 of 143286 triangles,
huter_corrected.pdb_j SES surface, 117834 of 119770 triangles,
huter_corrected.pdb_k SES surface, 9781 of 115294 triangles,
huter_corrected.pdb_l SES surface, 189 of 141304 triangles,
huter_corrected.pdb_n SES surface, 80956 of 127810 triangles,
huter_corrected.pdb_o SES surface, 15188 of 102000 triangles,
huter_corrected.pdb_p SES surface, 21529 of 87966 triangles,
huter_corrected.pdb_q SES surface, 2230 of 92162 triangles,
huter_corrected.pdb_r SES surface, 52542 of 76018 triangles,
huter_corrected.pdb_u SES surface, 59267 of 95002 triangles, 5mdv.pdb_2 SES
surface, 1348553 of 3959882 triangles, 5mdv.pdb_g SES surface, 5mdv.pdb_h SES
surface, 201975 of 203036 triangles, 5mdv.pdb_i SES surface, 199138 of 201386
triangles, 5mdv.pdb_j SES surface, 137505 of 137596 triangles, 5mdv.pdb_k SES
surface, 24615 of 107038 triangles, 5mdv.pdb_l SES surface, 83648 of 152700
triangles, 5mdv.pdb_m SES surface, 120176 of 120284 triangles, 5mdv.pdb_n SES
surface, 120507 of 132604 triangles, 5mdv.pdb_o SES surface, 107565 of 109548
triangles, 5mdv.pdb_p SES surface, 7940 of 119452 triangles, 5mdv.pdb_q SES
surface, 98 of 133776 triangles, 5mdv.pdb_s SES surface, 80107 of 122606
triangles, 5mdv.pdb_t SES surface, 15114 of 97168 triangles, 5mdv.pdb_u SES
surface, 19034 of 85776 triangles, 5mdv.pdb_v SES surface, 2745 of 93224
triangles, 5mdv.pdb_w SES surface, 49182 of 73420 triangles, 5mdv.pdb_z SES
surface, 68781 of 105428 triangles, 5mdw.pdb_2 SES surface, 1339375 of 3965800
triangles, 5mdw.pdb_g SES surface, 5mdw.pdb_h SES surface, 201223 of 202820
triangles, 5mdw.pdb_i SES surface, 200720 of 203256 triangles, 5mdw.pdb_j SES
surface, 137569 of 137766 triangles, 5mdw.pdb_k SES surface, 25565 of 109036
triangles, 5mdw.pdb_l SES surface, 83803 of 151702 triangles, 5mdw.pdb_m SES
surface, 119055 of 119168 triangles, 5mdw.pdb_n SES surface, 120805 of 133036
triangles, 5mdw.pdb_o SES surface, 108443 of 110766 triangles, 5mdw.pdb_p SES
surface, 9258 of 119092 triangles, 5mdw.pdb_q SES surface, 119 of 133904
triangles, 5mdw.pdb_s SES surface, 76674 of 121474 triangles, 5mdw.pdb_t SES
surface, 14592 of 96506 triangles, 5mdw.pdb_u SES surface, 19248 of 86502
triangles, 5mdw.pdb_v SES surface, 2724 of 92660 triangles, 5mdw.pdb_w SES
surface, 51086 of 74906 triangles, 5mdw.pdb_z SES surface, 69204 of 105044
triangles, 6szs.pdb_a SES surface, 1365192 of 3953176 triangles, 6szs.pdb_b
SES surface, 6szs.pdb_c SES surface, 201278 of 201842 triangles, 6szs.pdb_d
SES surface, 198461 of 200376 triangles, 6szs.pdb_e SES surface, 139918 of
140070 triangles, 6szs.pdb_f SES surface, 18099 of 100246 triangles,
6szs.pdb_g SES surface, 81785 of 147750 triangles, 6szs.pdb_h SES surface,
119973 of 120106 triangles, 6szs.pdb_i SES surface, 121684 of 133526
triangles, 6szs.pdb_j SES surface, 111063 of 113196 triangles, 6szs.pdb_k SES
surface, 7643 of 115982 triangles, 6szs.pdb_l SES surface, 168 of 134408
triangles, 6szs.pdb_n SES surface, 83788 of 126616 triangles, 6szs.pdb_o SES
surface, 14123 of 95042 triangles, 6szs.pdb_p SES surface, 19631 of 88464
triangles, 6szs.pdb_q SES surface, 2506 of 89452 triangles, 6szs.pdb_r SES
surface, 49601 of 74634 triangles, 6szs.pdb_u SES surface, 67133 of 104534
triangles
> select clear
> select #14/a:999@O2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
33016 atoms, 36967 bonds, 1539 residues, 2 models selected
> select clear
Drag select of huter_corrected.pdb_a SES surface, 687710 of 4003356 triangles,
huter_corrected.pdb_b SES surface, huter_corrected.pdb_c SES surface, 190062
of 209098 triangles, huter_corrected.pdb_d SES surface, 142449 of 209444
triangles, huter_corrected.pdb_e SES surface, 113519 of 142936 triangles,
huter_corrected.pdb_g SES surface, 32225 of 158486 triangles,
huter_corrected.pdb_h SES surface, 100717 of 123984 triangles,
huter_corrected.pdb_i SES surface, 117465 of 143286 triangles,
huter_corrected.pdb_j SES surface, 103687 of 119770 triangles,
huter_corrected.pdb_n SES surface, 35753 of 127810 triangles,
huter_corrected.pdb_o SES surface, 19 of 102000 triangles,
huter_corrected.pdb_p SES surface, 868 of 87966 triangles,
huter_corrected.pdb_r SES surface, 16870 of 76018 triangles,
huter_corrected.pdb_u SES surface, 17066 of 95002 triangles, 5mdv.pdb_2 SES
surface, 685123 of 3959882 triangles, 5mdv.pdb_g SES surface, 5mdv.pdb_h SES
surface, 183698 of 203036 triangles, 5mdv.pdb_i SES surface, 134469 of 201386
triangles, 5mdv.pdb_j SES surface, 108848 of 137596 triangles, 5mdv.pdb_k SES
surface, 1375 of 107038 triangles, 5mdv.pdb_l SES surface, 28609 of 152700
triangles, 5mdv.pdb_m SES surface, 97767 of 120284 triangles, 5mdv.pdb_n SES
surface, 107108 of 132604 triangles, 5mdv.pdb_o SES surface, 93893 of 109548
triangles, 5mdv.pdb_s SES surface, 35070 of 122606 triangles, 5mdv.pdb_u SES
surface, 878 of 85776 triangles, 5mdv.pdb_w SES surface, 16047 of 73420
triangles, 5mdv.pdb_z SES surface, 28093 of 105428 triangles, 5mdw.pdb_2 SES
surface, 680427 of 3965800 triangles, 5mdw.pdb_g SES surface, 5mdw.pdb_h SES
surface, 182344 of 202820 triangles, 5mdw.pdb_i SES surface, 134496 of 203256
triangles, 5mdw.pdb_j SES surface, 107988 of 137766 triangles, 5mdw.pdb_k SES
surface, 1534 of 109036 triangles, 5mdw.pdb_l SES surface, 29237 of 151702
triangles, 5mdw.pdb_m SES surface, 96902 of 119168 triangles, 5mdw.pdb_n SES
surface, 107445 of 133036 triangles, 5mdw.pdb_o SES surface, 94497 of 110766
triangles, 5mdw.pdb_s SES surface, 33781 of 121474 triangles, 5mdw.pdb_u SES
surface, 934 of 86502 triangles, 5mdw.pdb_w SES surface, 16901 of 74906
triangles, 5mdw.pdb_z SES surface, 28295 of 105044 triangles, 6szs.pdb_a SES
surface, 685478 of 3953176 triangles, 6szs.pdb_b SES surface, 6szs.pdb_c SES
surface, 182709 of 201842 triangles, 6szs.pdb_d SES surface, 134225 of 200376
triangles, 6szs.pdb_e SES surface, 112532 of 140070 triangles, 6szs.pdb_f SES
surface, 333 of 100246 triangles, 6szs.pdb_g SES surface, 27540 of 147750
triangles, 6szs.pdb_h SES surface, 97043 of 120106 triangles, 6szs.pdb_i SES
surface, 106795 of 133526 triangles, 6szs.pdb_j SES surface, 97631 of 113196
triangles, 6szs.pdb_n SES surface, 36183 of 126616 triangles, 6szs.pdb_p SES
surface, 698 of 88464 triangles, 6szs.pdb_r SES surface, 16085 of 74634
triangles, 6szs.pdb_u SES surface, 26376 of 104534 triangles
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
Drag select of huter_corrected.pdb_a SES surface, 10544 of 4003356 triangles,
huter_corrected.pdb_l SES surface, 6384 of 141304 triangles,
huter_corrected.pdb_q SES surface, 6961 of 92162 triangles, 5mdv.pdb_2 SES
surface, 10722 of 3959882 triangles, 5mdv.pdb_q SES surface, 5341 of 133776
triangles, 5mdv.pdb_v SES surface, 7426 of 93224 triangles, 5mdw.pdb_2 SES
surface, 10515 of 3965800 triangles, 5mdw.pdb_q SES surface, 4922 of 133904
triangles, 5mdw.pdb_v SES surface, 7255 of 92660 triangles, 6szs.pdb_a SES
surface, 10312 of 3953176 triangles, 6szs.pdb_l SES surface, 5610 of 134408
triangles, 6szs.pdb_q SES surface, 5725 of 89452 triangles
> select clear
> select #16/x:26@CA
1 atom, 1 residue, 1 model selected
> select add #14/s:23@CB
2 atoms, 2 residues, 3 models selected
> select add #16/q:37@CB
3 atoms, 3 residues, 4 models selected
> select add #14/l:35@NH1
4 atoms, 4 residues, 5 models selected
> select add #16/q:75@NE2
5 atoms, 5 residues, 6 models selected
> select add #14/m:53@OD1
6 atoms, 6 residues, 6 models selected
> select add #16/r:55@CG2
7 atoms, 7 residues, 7 models selected
> select add #16/y:45@CB
8 atoms, 8 residues, 8 models selected
> select add #14/t:48@CE
9 atoms, 9 residues, 9 models selected
> select add #15/v:50@ND2
10 atoms, 10 residues, 11 models selected
> select add #17/q:52@O
11 atoms, 11 residues, 13 models selected
> select add #17/o:76@CB
12 atoms, 12 residues, 14 models selected
> select add #15/t:79@CG2
13 atoms, 13 residues, 15 models selected
> select add #14/f:73@OE1
14 atoms, 14 residues, 16 models selected
> select up
107 atoms, 93 bonds, 14 residues, 17 models selected
> select up
1142 atoms, 1140 bonds, 144 residues, 17 models selected
> select up
9870 atoms, 10012 bonds, 1245 residues, 17 models selected
> select up
574411 atoms, 622966 bonds, 42430 residues, 17 models selected
> select down
9870 atoms, 10012 bonds, 1245 residues, 216 models selected
> color sel lemon chiffon
> select clear
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> select #17/l:37@CB
1 atom, 1 residue, 1 model selected
> select add #17/s:24@O
2 atoms, 2 residues, 2 models selected
> select add #17/m:62@CE
3 atoms, 3 residues, 2 models selected
> select add #17/t:8@NZ
4 atoms, 4 residues, 4 models selected
> select add #17/k:105@CZ
5 atoms, 5 residues, 5 models selected
> show #!2 models
> hide #!2 models
> select up
45 atoms, 41 bonds, 5 residues, 6 models selected
> select up
588 atoms, 590 bonds, 73 residues, 6 models selected
> select up
4048 atoms, 4110 bonds, 523 residues, 6 models selected
> color sel lemon chiffon
> select clear
> hide #!17 models
> show #!16 models
> select add #16/t:26@CB
1 atom, 1 residue, 1 model selected
> select add #16/v:77@CA
2 atoms, 2 residues, 2 models selected
> select up
20 atoms, 18 bonds, 2 residues, 3 models selected
> select up
239 atoms, 242 bonds, 30 residues, 3 models selected
> select up
1362 atoms, 1379 bonds, 168 residues, 3 models selected
> color sel lemon chiffon
> select clear
> show #!15 models
> hide #!16 models
> select add #15/y:49@CE
1 atom, 1 residue, 1 model selected
> select add #15/q:37@CG1
2 atoms, 2 residues, 2 models selected
> select add #15/x:23@CG1
3 atoms, 3 residues, 3 models selected
> select add #15/r:55@CG2
4 atoms, 4 residues, 4 models selected
> select add #15/p:104@CA
5 atoms, 5 residues, 5 models selected
> select up
34 atoms, 29 bonds, 5 residues, 6 models selected
> select up
496 atoms, 496 bonds, 63 residues, 6 models selected
> select up
4066 atoms, 4128 bonds, 525 residues, 6 models selected
> color sel lemon chiffon
> select clear
> show #!14 models
> hide #!15 models
> select add #14/q:51@CA
1 atom, 1 residue, 1 model selected
> select add #14/k:15@CG2
2 atoms, 2 residues, 2 models selected
> select up
16 atoms, 14 bonds, 2 residues, 3 models selected
> select up
114 atoms, 112 bonds, 15 residues, 3 models selected
> select up
1517 atoms, 1542 bonds, 196 residues, 3 models selected
> color sel lemon chiffon
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> open C:\Users\claud\Downloads\5mgp-pdb-bundle.tar\5mgp-pdb-
> bundle\huter_corrected.pdb format pdb
Summary of feedback from opening C:\Users\claud\Downloads\5mgp-pdb-
bundle.tar\5mgp-pdb-bundle\huter_corrected.pdb
---
warning | Ignored bad PDB record found on line 147218
END
Chain information for huter_corrected.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
6 | No description available
A | No description available
B | No description available
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x | No description available
z | No description available
> ui tool show Matchmaker
> matchmaker #1/A to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with huter_corrected.pdb, chain A
(#1), sequence alignment score = 11493.7
RMSD between 2391 pruned atom pairs is 1.238 angstroms; (across all 2900
pairs: 1.846)
> hide #!14 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!1 cartoons
> hide #!1 atoms
> select #1/z:129
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/x:10
35 atoms, 37 bonds, 2 residues, 1 model selected
> select add #1/w:24
43 atoms, 44 bonds, 3 residues, 1 model selected
> select add #1/v:16
63 atoms, 65 bonds, 4 residues, 1 model selected
> select up
1849 atoms, 2056 bonds, 92 residues, 1 model selected
> select up
4987 atoms, 5239 bonds, 487 residues, 1 model selected
> select ~sel
1018378 atoms, 1104452 bonds, 4 pseudobonds, 75272 residues, 28 models
selected
> ~select #2
873488 atoms, 947629 bonds, 4 pseudobonds, 64298 residues, 354 models selected
> ~select #5
727017 atoms, 789038 bonds, 4 pseudobonds, 53250 residues, 281 models selected
> ~select #11
716694 atoms, 777589 bonds, 4 pseudobonds, 52689 residues, 224 models selected
> ~select #13
716579 atoms, 777475 bonds, 4 pseudobonds, 52666 residues, 220 models selected
> ~select #14
574411 atoms, 622966 bonds, 2 pseudobonds, 42430 residues, 217 models selected
> ~select #15
429490 atoms, 466117 bonds, 2 pseudobonds, 31455 residues, 164 models selected
> ~select #16
284581 atoms, 309279 bonds, 2 pseudobonds, 20483 residues, 109 models selected
> ~select #17
142168 atoms, 154509 bonds, 2 pseudobonds, 10236 residues, 54 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> hide #!1 models
> open C:\Users\claud\Downloads\5mdv-pdb-bundle.tar\5mdv-pdb-bundle\5mdv.pdb
> format pdb
Summary of feedback from opening C:\Users\claud\Downloads\5mdv-pdb-
bundle.tar\5mdv-pdb-bundle\5mdv.pdb
---
warning | Ignored bad PDB record found on line 151407
END
Chain information for 5mdv.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
C | No description available
D | No description available
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F | No description available
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w | No description available
x | No description available
y | No description available
z | No description available
> ui tool show Matchmaker
> show #!2 models
> matchmaker #3/1 to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with 5mdv.pdb, chain 1 (#3), sequence
alignment score = 11581.2
RMSD between 2237 pruned atom pairs is 1.314 angstroms; (across all 2903
pairs: 1.819)
> show #3#!2 cartoons
> hide #3#!2 surfaces
> hide #3#!2 atoms
> hide #!2 models
> open C:\Users\claud\Downloads\5mdw-pdb-bundle.tar\5mdw-pdb-bundle\5mdw.pdb
> format pdb
Summary of feedback from opening C:\Users\claud\Downloads\5mdw-pdb-
bundle.tar\5mdw-pdb-bundle\5mdw.pdb
---
warning | Ignored bad PDB record found on line 151107
END
Chain information for 5mdw.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
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V | No description available
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c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
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l | No description available
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p | No description available
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t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> show #3#!4 cartoons
> hide #3#!4 atoms
> ui tool show Matchmaker
> matchmaker #4/1 to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with 5mdw.pdb, chain 1 (#4), sequence
alignment score = 11581.2
RMSD between 2323 pruned atom pairs is 1.304 angstroms; (across all 2903
pairs: 1.686)
> hide #3 models
> hide #!4 models
> show #!2 models
> open C:\Users\claud\Downloads\6szs-pdb-bundle.tar\6szs-pdb-bundle\6szs.pdb
> format pdb
Summary of feedback from opening C:\Users\claud\Downloads\6szs-pdb-
bundle.tar\6szs-pdb-bundle\6szs.pdb
---
warning | Ignored bad PDB record found on line 147968
END
Chain information for 6szs.pdb #6
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
x | No description available
y | No description available
z | No description available
> show #6#!2 cartoons
> hide #6#!2 atoms
> ui tool show Matchmaker
> matchmaker #6/A to #2/1 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6q97_A-site.pdb, chain 1 (#2) with 6szs.pdb, chain A (#6), sequence
alignment score = 11514.7
RMSD between 2325 pruned atom pairs is 1.300 angstroms; (across all 2903
pairs: 1.806)
> hide #!2 models
> show #!4 models
> show #3 models
> show #!1 models
> hide #!1 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> select #6/y:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/7:310
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #6/z:308
25 atoms, 22 bonds, 3 residues, 2 models selected
> select add #4/7:299
34 atoms, 30 bonds, 4 residues, 3 models selected
> select add #4/6:19
42 atoms, 37 bonds, 5 residues, 3 models selected
> select add #3/6:18
47 atoms, 41 bonds, 6 residues, 3 models selected
Drag select of 9 residues
> select add #6/v:13
266 atoms, 62 bonds, 16 residues, 3 models selected
> select add #3/4:14
288 atoms, 86 bonds, 17 residues, 3 models selected
> select add #4/4:14
310 atoms, 110 bonds, 18 residues, 3 models selected
> select up
6213 atoms, 6825 bonds, 363 residues, 3 models selected
> select up
14643 atoms, 15380 bonds, 1450 residues, 3 models selected
> select ~sel
1313414 atoms, 1423621 bonds, 2 pseudobonds, 97709 residues, 30 models
selected
> ~select #1
1308427 atoms, 1418382 bonds, 2 pseudobonds, 97222 residues, 356 models
selected
> ~select #2
1163537 atoms, 1261559 bonds, 2 pseudobonds, 86248 residues, 355 models
selected
> ~select #5
1017066 atoms, 1102968 bonds, 2 pseudobonds, 75200 residues, 282 models
selected
> ~select #11
1006743 atoms, 1091519 bonds, 2 pseudobonds, 74639 residues, 225 models
selected
> ~select #13
1006628 atoms, 1091405 bonds, 2 pseudobonds, 74616 residues, 221 models
selected
> ~select #14
864460 atoms, 936896 bonds, 64380 residues, 218 models selected
> ~select #15
719539 atoms, 780047 bonds, 53405 residues, 165 models selected
> ~select #16
574630 atoms, 623209 bonds, 42433 residues, 110 models selected
> ~select #17
432217 atoms, 468439 bonds, 32186 residues, 55 models selected
> delete atoms sel
> delete bonds sel
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!1 models
> hide #6 models
> show #6 models
> show #3,6#!1,4 surfaces
> hide #!1,3-4,6 cartoons
> hide #!6 models
Drag select of huter_corrected.pdb_x SES surface, 51574 of 220318 triangles,
5mdv.pdb_5 SES surface, 51584 of 218068 triangles, 5mdw.pdb_5 SES surface,
51768 of 218916 triangles
Drag select of huter_corrected.pdb_x SES surface, 34495 of 220318 triangles,
5mdv.pdb_5 SES surface, 32078 of 218068 triangles, 5mdw.pdb_5 SES surface,
32427 of 218916 triangles
> color sel forest green
> select clear
Drag select of huter_corrected.pdb_z SES surface, 42514 of 388472 triangles,
5mdv.pdb_7 SES surface, 36964 of 356716 triangles, 5mdw.pdb_7 SES surface,
63541 of 325306 triangles
> color sel orange red
> color sel coral
> color sel orange
> color sel orange
> color sel dark orange
> color sel coral
> color sel dark orange
> color sel peach puff
> color sel navajo white
> color sel orange
> color sel dark orange
Drag select of huter_corrected.pdb_v SES surface, 7715 of 23030 triangles,
5mdv.pdb_4 SES surface, 3376 of 19394 triangles, 5mdw.pdb_4 SES surface, 3442
of 19382 triangles
> color sel deep sky blue
Drag select of huter_corrected.pdb_w SES surface, 7191 of 70914 triangles,
5mdv.pdb_6 SES surface, 6635 of 70600 triangles, 5mdw.pdb_6 SES surface, 7179
of 52276 triangles
> color sel crimson
> color sel red
> color sel crimson
> color sel red
> color sel fire brick
> color sel indian red
> color sel pale violet red
> color sel crimson
> color sel red
> color sel crimson
Drag select of huter_corrected.pdb_v SES surface, 7611 of 23030 triangles,
5mdv.pdb_4 SES surface, 3747 of 19394 triangles, 5mdw.pdb_4 SES surface, 3887
of 19382 triangles
> color sel cyan
> color sel deep sky blue
> select clear
Drag select of huter_corrected.pdb_v SES surface, 7725 of 23030 triangles,
5mdv.pdb_4 SES surface, 3886 of 19394 triangles, 5mdw.pdb_4 SES surface, 3931
of 19382 triangles
> color sel cyan
> select clear
> hide #!3 models
> hide #!1 models
> show #!4 cartoons
> hide #!4 surfaces
> show #!4 surfaces
> hide #!4 cartoons
> hide #!4 models
> show #!6 models
Drag select of 6szs.pdb_v SES surface, 1737 of 22602 triangles
Drag select of 6szs.pdb_v SES surface, 2465 of 22602 triangles
> color sel cyan
Drag select of 6szs.pdb_x SES surface, 61055 of 216632 triangles
> color sel forest green
Drag select of 6szs.pdb_z SES surface, 37693 of 344668 triangles
> color sel teal
> color sel deep sky blue
> color sel coral
> color sel peru
> color sel tomato
> color sel dark orange
> color sel tomato
> color sel plum
> color sel rosy brown
> color sel aquamarine
> color sel light sky blue
> color sel sky blue
> color sel pale turquoise
> color sel silver
> color sel dark orchid
> color sel dark magenta
> color sel rebecca purple
> color sel dark olive green
> color sel yellow
> color sel coral
> show #!3 models
> hide #!3 models
> color sel salmon
> show #!3 models
> hide #!3 models
> color sel chocolate
> show #!3 models
> hide #!3 models
> color sel saddle brown
> color sel brown
> color sel fire brick
> color sel indian red
> show #!3 models
> hide #!3 models
> color sel fire brick
> color sel maroon
> color sel dark red
> color sel brown
> color sel dark red
> color sel fire brick
> color sel crimson
> color sel dark cyan
> color sel dark turquoise
> color sel dodger blue
> color sel turquoise
> color sel slate blue
> color sel light coral
> color sel thistle
> color sel pale violet red
> color sel hot pink
> color sel magenta
> color sel deep pink
> color sel cornflower blue
> color sel yellow
> color sel gold
> show #!3 models
> hide #!3 models
Drag select of 6szs.pdb_y SES surface, 4355 of 83380 triangles
> color sel cornflower blue
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> select clear
Drag select of 6szs.pdb_z SES surface, 17718 of 344668 triangles
> color sel indian red
> color sel dark red
> color sel brown
> show #!3 models
> hide #!3 models
> color sel saddle brown
> color sel sienna
> color sel chocolate
> color sel saddle brown
> color sel sienna
> select clear
> sharpBoundaries true
Unknown command: sharpBoundaries true
> sharpBoundaries, true
Unknown command: sharpBoundaries, true
> surface sharpBoundaries true
> show #!4 models
> hide #!6 models
> surface sharpBoundaries true
> show #!6 models
> hide #!4 models
> show #!6 cartoons
> hide #!6 surfaces
> show #!6 atoms
> style #!6 stick
Changed 4948 atom styles
> show #!3 models
> hide #!6 models
> hide #!3 surfaces
> show #!3 atoms
> style #!3 stick
Changed 4985 atom styles
> show #!3 cartoons
> show #!3 surfaces
> hide #!3 surfaces
> hide #!3 surfaces
> show #!3 surfaces
> hide #!3 cartoons
> hide #!3 atoms
> show #!6 models
> show #!3,6 surfaces
> hide #!3,6 atoms
> hide #!3,6 cartoons
> hide #!6 models
> hide #!3 models
> show #!4 models
> view name 3
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> view 2
> view 3
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!17 models
> hide #!17 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!1 cartoons
> hide #!1 surfaces
> select clear
> show #!4 models
> hide #!1,4 surfaces
> show #!1,4 cartoons
Drag select of 99 residues
> select up
1433 atoms, 1444 bonds, 180 residues, 4 models selected
> select up
5552 atoms, 5627 bonds, 700 residues, 4 models selected
> color sel dark orange
Drag select of 16 residues
> select up
344 atoms, 346 bonds, 42 residues, 4 models selected
> select up
630 atoms, 640 bonds, 77 residues, 4 models selected
> color sel crimson
> color sel red
> color sel crimson
> select clear
Drag select of 1 residues
Drag select of 3 residues
> select up
235 atoms, 261 bonds, 11 residues, 4 models selected
> color sel cyan
> select clear
Drag select of 13 residues
Drag select of 21 residues
> select up
3268 atoms, 3650 bonds, 153 residues, 4 models selected
> color sel forest green
> select clear
> hide #!4 models
> hide #!1 models
> show #!6 models
> hide #!6 surfaces
> show #!6 cartoons
Drag select of 34 residues
> color sel sienna
> select clear
Drag select of 73 residues
> select up
682 atoms, 687 bonds, 96 residues, 2 models selected
> select up
2742 atoms, 2786 bonds, 362 residues, 2 models selected
> color sel sienna
Drag select of 9 residues
> select up
134 atoms, 136 bonds, 15 residues, 2 models selected
> select up
434 atoms, 440 bonds, 54 residues, 2 models selected
> color sel cornflower blue
Drag select of 21 residues
> select up
1646 atoms, 1839 bonds, 77 residues, 2 models selected
> color sel forest green
Drag select of 2 residues
> select up
126 atoms, 139 bonds, 6 residues, 2 models selected
> color sel cyan
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!4 models
> show #!1 models
> cartoon style #1,4,6 modeHelix tube sides 20
> hide #!6 models
> hide #!1 models
> cartoon style #4 xsection oval modeHelix default
> cartoon style #4 modeHelix tube sides 20
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
——— End of log from Wed Nov 11 01:27:39 2020 ———
opened ChimeraX session
> setattr #4/6:27-30 res ss_type 2
Assigning ss_type attribute to 4 items
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> setattr #1/w:27-30 res ss_type 2
Assigning ss_type attribute to 4 items
> hide #!1 models
> show #!3 models
> hide #!3 surfaces
> show #!3 cartoons
> setattr #3/6:27-30 res ss_type 2
Assigning ss_type attribute to 4 items
Drag select of 41 residues
> select up
616 atoms, 621 bonds, 77 residues, 2 models selected
> select up
2863 atoms, 2903 bonds, 362 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
Drag select of 2 residues
> select clear
Drag select of 3 residues
> select up
125 atoms, 126 bonds, 16 residues, 2 models selected
> select up
377 atoms, 383 bonds, 46 residues, 2 models selected
> color sel crimson
> select clear
Drag select of 20 residues
> select up
1622 atoms, 1811 bonds, 76 residues, 2 models selected
> color sel forest green
> select #3/4:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
109 atoms, 122 bonds, 5 residues, 2 models selected
> color sel cyan
> select clear
> hide #!3 models
> show #!6 models
> setattr #6/y:35-38 res ss_type 2
Assigning ss_type attribute to 4 items
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!4 models
> hide #!4 models
> show #!3 models
> cartoon style #3,6 modeHelix tube sides 20
> hide #!3 models
> view 2
> ui tool show "Side View"
> view 1
> show #!6 surfaces
> hide #!6 cartoons
> hide #!6 models
> show #!3 models
> show #!3 surfaces
> hide #!3 models
> show #!4 models
> show #!4 surfaces
> hide #!4 surfaces
> show #!3 models
> hide #!3-4 surfaces
> show #!6 models
> hide #!3-4,6 surfaces
> show #!3-4,6 cartoons
> hide #!3 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> show #!4 models
> show #!3 models
> show #!3-4,6 surfaces
> hide #!3 models
> hide #!4 models
> hide #!6 models
> show #!15 models
> view 1
> view 1
> view 2
> save C:\Users\claud\Desktop\image1.png supersample 3
> save C:\Users\claud\Desktop\image2.png supersample 3
> show #!16 models
> hide #!15 models
> save C:\Users\claud\Desktop\image2.png supersample 3
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> save C:\Users\claud\Desktop\image3.png supersample 3
> hide #!17 models
> show #!3 models
> save C:\Users\claud\Desktop\image4.png supersample 3
> hide #!3 models
> show #!4 models
> save C:\Users\claud\Desktop\image5.png supersample 3
> hide #!4 models
> show #!6 models
> save C:\Users\claud\Desktop\image6.png supersample 3
> view 1
> hide #!6 models
> show #!3 models
> save C:\Users\claud\Desktop\image4.png supersample 3
> show #!4 models
> hide #!3 models
> save C:\Users\claud\Desktop\image5.png supersample 3
> hide #!4 models
> show #!6 models
> save C:\Users\claud\Desktop\image6.png supersample 3
> hide #!6 models
> show #!4 models
Drag select of 5mdw.pdb_6 SES surface, 16161 of 52276 triangles, 5mdw.pdb_7
SES surface, 6173 of 325306 triangles, 16 residues
> select up
306 atoms, 308 bonds, 38 residues, 3 models selected
> select up
2967 atoms, 3006 bonds, 373 residues, 3 models selected
> hide sel surfaces
> hide sel cartoons
> select clear
> save C:\Users\claud\Desktop\image7.png supersample 3
> show #!4 cartoons
> hide #!4 surfaces
> select clear
> show #!3 models
> hide #!3-4 surfaces
> hide #!3 models
Drag select of 10 residues
> select up
125 atoms, 126 bonds, 16 residues, 2 models selected
> select up
261 atoms, 265 bonds, 32 residues, 2 models selected
> hide sel cartoons
> view name 4
> select #4/7:97
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
209 atoms, 210 bonds, 26 residues, 2 models selected
> select up
2706 atoms, 2741 bonds, 341 residues, 2 models selected
> color (#!4 & sel) light gray
> color (#!4 & sel) dim gray
> ui tool show "Color Actions"
> color sel gray
> color sel silver
> color sel gray
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> transparency #4/7 50 cartoons
> transparency #4/7 40 cartoons
> transparency #4/7 60 cartoons
> show #!3 models
> transparency #4/7 70 cartoons
> view 4
> save C:\Users\claud\Desktop\image8.png supersample 3
Drag select of 5 residues
> select up
125 atoms, 126 bonds, 16 residues, 2 models selected
> select up
377 atoms, 383 bonds, 46 residues, 2 models selected
> hide sel cartoons
> view 4
> save C:\Users\claud\Desktop\image8.png supersample 3
> view name 5
> save C:\Users\claud\Desktop\image9.png supersample 3
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
Drag select of 21 residues
> select up
1731 atoms, 1933 bonds, 81 residues, 3 models selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show #!3 models
> save C:\Users\claud\Desktop\image9.png supersample 3
> hide #!4 models
> show #!3 cartoons
> show #!4 models
> hide #!3 models
> show sel cartoons
> show sel cartoons
> select clear
> show #!4 cartoons
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!3 models
> show #!6 models
> hide #!3-4,6 surfaces
> hide #!6 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> select clear
> transparency #4/7 0 cartoons
Drag select of 25 residues
> select up
498 atoms, 502 bonds, 63 residues, 2 models selected
> select up
2706 atoms, 2741 bonds, 341 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> view name 6
> save C:\Users\claud\Desktop\image10.png supersample 3
> hide #!4 models
> show #!3 models
> save C:\Users\claud\Desktop\image11.png supersample 3
> hide #!3 models
> show #!6 models
> save C:\Users\claud\Desktop\image12.png supersample 3
> view 6
> hide #!6 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> view 6
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> view name 7
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> view 6
> view 5
> view 4
> view 7
> view 6
> hide #!6 models
> show #!17 models
> show #!6 models
> hide #!6 models
> view name 8
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!6 models
> hide #!6 models
> hide #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> hide #!14 models
> show #!16 models
> view
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> select #16/p:105@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
49 atoms, 49 bonds, 6 residues, 2 models selected
> select up
877 atoms, 893 bonds, 117 residues, 2 models selected
> color sel lemon chiffon
> select clear
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> view 8
> hide #!16 models
> show #!3 models
> view 7
> view 8
> view name 9
> save C:\Users\claud\Desktop\image13.png supersample 3
> view 6
> hide #!3 models
> show #!4 models
> save C:\Users\claud\Desktop\image14.png supersample 3
> hide #!4 models
> show #!6 models
> hide #!6 models
> view 8
> show #!15 models
> save C:\Users\claud\Desktop\image13.png supersample 3
> hide #!15 models
> show #!16 models
> save C:\Users\claud\Desktop\image14.png supersample 3
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> save C:\Users\claud\Desktop\image15.png supersample 3
> show #!6 models
> hide #!6 models
> hide #!17 models
> view 6
> show #!6 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> select #17
142413 atoms, 154770 bonds, 10247 residues, 51 models selected
> ~select #17
52 models selected
> select #6
4948 atoms, 5204 bonds, 499 residues, 1 model selected
> ui tool show "Build Structure"
> toolshed show
> select clear
> setattr #6/z:26-40 res ss_type 1
Assigning ss_type attribute to 15 items
> setattr #6/z:26-40 res ss_type 0
Assigning ss_type attribute to 15 items
> setattr #6/z:26-40 res ss_type 1
Assigning ss_type attribute to 15 items
> setattr #6/z:44-47 res ss_type 1
Assigning ss_type attribute to 4 items
> setattr #6/z:321-326 res ss_type 0
Assigning ss_type attribute to 6 items
> setattr #6/z:321-325 res ss_type 2
Assigning ss_type attribute to 5 items
> setattr #6/z:321-325 res ss_type 0
Assigning ss_type attribute to 5 items
> setattr #6/z:321-324 res ss_type 2
Assigning ss_type attribute to 4 items
> setattr #6/z:321-325 res ss_type 0
Assigning ss_type attribute to 5 items
> setattr #6/z:323-326 res ss_type 2
Assigning ss_type attribute to 4 items
> setattr #6/z:332-3335 res ss_type 2
Assigning ss_type attribute to 35 items
> setattr #6/z:332-3335 res ss_type 0
Assigning ss_type attribute to 35 items
> setattr #6/z:332-335 res ss_type 2
Assigning ss_type attribute to 4 items
> setattr #6/z:332-336 res ss_type 2
Assigning ss_type attribute to 5 items
> setattr #6/z:332-336 res ss_type 0
Assigning ss_type attribute to 5 items
> setattr #6/z:332-335 res ss_type 2
Assigning ss_type attribute to 4 items
> setattr #6/z:340-343 res ss_type 2
Assigning ss_type attribute to 4 items
> setattr #6/z:332-336 res ss_type 2
Assigning ss_type attribute to 5 items
> setattr #6/z:332-336 res ss_type 0
Assigning ss_type attribute to 5 items
> setattr #6/z:332-335 res ss_type 2
Assigning ss_type attribute to 4 items
> setattr #6/z:340-343 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #6/z:341-343 res ss_type 2
Assigning ss_type attribute to 3 items
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> setattr #6/z:346-350 res ss_type 1
Assigning ss_type attribute to 5 items
> setattr #6/z:354-365 res ss_type 1
Assigning ss_type attribute to 12 items
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> show #!3 models
Drag select of 27 residues
> select up
3503 atoms, 3911 bonds, 164 residues, 6 models selected
> hide sel cartoons
> select clear
> setattr #6/z:175-179 res ss_type 0
Assigning ss_type attribute to 5 items
> setattr #6/z:177-183 res ss_type 2
Assigning ss_type attribute to 7 items
> setattr #6/z:166-169 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #6/z:161-168 res ss_type 2
Assigning ss_type attribute to 8 items
> setattr #6/z:160-168 res ss_type 2
Assigning ss_type attribute to 9 items
> setattr #6/z:160-168 res ss_type 0
Assigning ss_type attribute to 9 items
> setattr #6/z:161-168 res ss_type 2
Assigning ss_type attribute to 8 items
> hide #!3 models
> show #!3 models
> hide #!3 models
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
> hide #!6 models
> show #!16 models
> view 2
> save C:\Users\claud\Desktop\image14.png supersample 3
> hide #!16 models
> show #!6 models
> view 7
> show #!6 cartoons
Drag select of 7 residues
> select down
153 atoms, 7 residues, 3 models selected
> select up
1772 atoms, 1978 bonds, 83 residues, 3 models selected
> hide sel cartoons
> view 7
> show #!3 models
> hide #!3 models
> save C:\Users\claud\Desktop\image14.png supersample 3
> hide #!6 models
> show #!3 models
> save C:\Users\claud\Desktop\image15.png supersample 3
> hide #!3 models
> show #!17 models
> show #!6 models
> hide #!6 models
> view name 9
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
——— End of log from Thu Nov 12 16:47:41 2020 ———
opened ChimeraX session
> hide #!17 models
> show #!3 models
> show #!4 models
> view 6
> view 6
> view 6
> view 6
> view 5
> view 4
> ui tool show "Side View"
> hide #!4 models
> view 9
> view 7
> select #3/6:44
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/6:45
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/6:44
19 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> color (#!3 & sel) byhetero
> select clear
> view 7
> save C:\Users\claud\Desktop\image14.png supersample 3
> show #!6 models
> hide #!3 models
> select clear
> select #6/y:50
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #6/y:49
19 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> color (#!6 & sel) byhetero
> select clear
> view 7
> save C:\Users\claud\Desktop\image15.png supersample 3
> view 1
> hide #!6 models
> show #!15 models
> surface gridSpacing 2
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
——— End of log from Fri Nov 13 01:13:06 2020 ———
opened ChimeraX session
> surface gridSpacing 2
> view 2
> ui tool show "Side View"
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> surface gridSpacing 2.5
> show #!14 models
> hide #!15 models
> show #!16 models
> hide #!14 models
> hide #!16 models
> show #!14 models
> hide #!14 models
> show #!1 models
> view 7
> show #!1 cartoons
> hide #!1 surfaces
> view 7
Drag select of 10 residues
> select up
1772 atoms, 1978 bonds, 83 residues, 3 models selected
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1,4 surfaces
> show #!1,4 cartoons
> hide #!4 models
> save C:\Users\claud\Desktop\image16.png supersample 3
> view 6
> view 5
> show #!3 models
> hide #!1,3 surfaces
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!4 models
> view 5
Drag select of 21 residues
> select up
1731 atoms, 1933 bonds, 81 residues, 3 models selected
> hide sel cartoons
Drag select of 3 residues
> select up
125 atoms, 126 bonds, 16 residues, 2 models selected
> select up
261 atoms, 265 bonds, 32 residues, 2 models selected
> hide sel cartoons
Drag select of 37 residues
> select up
530 atoms, 537 bonds, 64 residues, 2 models selected
> select up
2706 atoms, 2741 bonds, 341 residues, 2 models selected
> color (#!4 & sel) gray
> transparency #4/7 70 cartoons
> select clear
> show #!1 models
Drag select of 1 residues
> select up
125 atoms, 126 bonds, 16 residues, 2 models selected
> select up
369 atoms, 375 bonds, 45 residues, 2 models selected
> hide sel cartoons
> save C:\Users\claud\Desktop\image17.png supersample 3
> hide #!4 models
> show sel cartoons
> select clear
Drag select of 18 residues
> select up
1772 atoms, 1978 bonds, 83 residues, 3 models selected
> hide sel cartoons
> view 6
> view 7
> select #1/w:45
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/w:44
19 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 19 atom styles
> color (#!1 & sel) byhetero
> select clear
> view 7
> save C:\Users\claud\Desktop\image18.png supersample 3
> hide #!1 models
> show #!14 models
> view 9
> show #!17 models
> hide #!14 models
> surface gridSpacing 2.5
> surface gridSpacing auto
Invalid "gridSpacing" argument: Expected a number
> surface cap subdevision 2
Expected true or false or a keyword
> surface cap subdevision s
Expected true or false or a keyword
> surface cap subdevision factor 2
Expected true or false or a keyword
> Cap subdivision 2
Unknown command: Cap subdivision 2
> Cap subdivision factor 2
Unknown command: Cap subdivision factor 2
> cap subdivision factor 2
Unknown command: cap subdivision factor 2
> show #!14 models
> hide #!17 models
> show #!17 models
> hide #!14 models
> show #!14 models
> hide #!17 models
> save C:\Users\claud\Desktop\image19.png supersample 3
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> view 2
> show #!15 models
> show #!16 models
> hide #!14 models
> view 2
> hide #!15 models
> surface cap true subdivision 2
> surface cap subdivision 2.0
> surface cap true subdivision 3
> surface cap subdivision 3.0
> surface cap true subdivision 4
> surface cap subdivision 4.0
> hide #!16 models
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> surface cap true subdivision 1
> surface cap subdivision 1.0
> show #!14 models
> hide #!16 models
> hide #!14 models
> show #!16 models
Drag select of 5mdw.pdb_1 SES surface, 721834 of 739660 triangles, 5mdw.pdb_2
SES surface, 384492 of 395818 triangles, 5mdw.pdb_3 SES surface, 12063 of
34666 triangles, 5mdw.pdb_B SES surface, 5mdw.pdb_C SES surface, 5mdw.pdb_D
SES surface, 5mdw.pdb_E SES surface, 3691 of 16744 triangles, 5mdw.pdb_F SES
surface, 5mdw.pdb_G SES surface, 5mdw.pdb_H SES surface, 5mdw.pdb_I SES
surface, 5mdw.pdb_J SES surface, 5mdw.pdb_K SES surface, 5mdw.pdb_L SES
surface, 16383 of 17410 triangles, 5mdw.pdb_M SES surface, 5mdw.pdb_N SES
surface, 5mdw.pdb_P SES surface, 5mdw.pdb_Q SES surface, 5mdw.pdb_R SES
surface, 5mdw.pdb_S SES surface, 5mdw.pdb_T SES surface, 5mdw.pdb_U SES
surface, 5mdw.pdb_V SES surface, 17130 of 17652 triangles, 5mdw.pdb_W SES
surface, 6511 of 8332 triangles, 5mdw.pdb_X SES surface, 5mdw.pdb_Y SES
surface, 5mdw.pdb_Z SES surface, 5mdw.pdb_a SES surface, 869 of 9286
triangles, 5mdw.pdb_b SES surface, 5mdw.pdb_c SES surface, 4695 of 6148
triangles, 5mdw.pdb_d SES surface, 5mdw.pdb_e SES surface, 5mdw.pdb_f SES
surface, 5mdw.pdb_g SES surface, 5mdw.pdb_h SES surface, 5mdw.pdb_i SES
surface, 5mdw.pdb_j SES surface, 5mdw.pdb_k SES surface, 5mdw.pdb_l SES
surface, 13975 of 14702 triangles, 5mdw.pdb_m SES surface, 5mdw.pdb_n SES
surface, 10372 of 12622 triangles, 5mdw.pdb_o SES surface, 5mdw.pdb_p SES
surface, 5mdw.pdb_q SES surface, 5mdw.pdb_r SES surface, 6163 of 12270
triangles, 5mdw.pdb_s SES surface, 11341 of 12338 triangles, 5mdw.pdb_t SES
surface, 5mdw.pdb_u SES surface, 5mdw.pdb_v SES surface, 5mdw.pdb_w SES
surface, 5mdw.pdb_x SES surface, 9419 of 9536 triangles, 5mdw.pdb_y SES
surface, 5mdw.pdb_z SES surface
> hide #!16.59 models
> show #!16.59 models
> select clear
> select #16
144909 atoms, 156838 bonds, 10972 residues, 36 models selected
> surface gridSpacing 2
> surface gridSpacing 1
> surface gridSpacing 2.7
> surface gridSpacing 2.8
> surface gridSpacing 2.9
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 165, in <lambda>
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 201, in _fill_tree
self._get_info(model, all_selected_models, part_selected_models)
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 274, in _get_info
bg_color = self._model_color(obj)
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 297, in _model_color
return model.single_color
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 385, in _get_single_color
return self.color if vc is None else most_common_color(vc)
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\chimerax\core\colors.py", line 759, in most_common_color
max_index = argmax(counts)
File "<__array_function__ internals>", line 5, in argmax
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\numpy\core\fromnumeric.py", line 1188, in argmax
return _wrapfunc(a, 'argmax', axis=axis, out=out)
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\numpy\core\fromnumeric.py", line 58, in _wrapfunc
return bound(*args, **kwds)
ValueError: attempt to get argmax of an empty sequence
Error processing trigger "new frame":
ValueError: attempt to get argmax of an empty sequence
File "C:\Program Files\ChimeraX 1.2.dev202011040611\bin\lib\site-
packages\numpy\core\fromnumeric.py", line 58, in _wrapfunc
return bound(*args, **kwds)
See log for complete Python traceback.
> surface gridSpacing 2.8
> surface gridSpacing 2.7
> surface gridSpacing 2.75
> surface gridSpacing 2.89
> surface gridSpacing 2.85
> surface gridSpacing 2.8
> surface gridSpacing 2.7
> select clear
> save C:\Users\claud\Desktop\image20.png supersample 3
> view 2
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure3_ArfA-BrfA.cxs"
——— End of log from Fri Nov 13 02:10:38 2020 ———
opened ChimeraX session
> close #3-5,11,13,15-16
> save "C:/Users/claud/Documents/Reviews/FrontiersReview-Translation
> regulation/Figures/CimeraSessions/ChmX_Figure4_ArfB.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in take_snapshot
data = {attr:getattr(self, attr) for attr in init_attrs}
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in <dictcomp>
data = {attr:getattr(self, attr) for attr in init_attrs}
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 565, in get_color
return self._colors[0]
TypeError: 'NoneType' object is not subscriptable
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface': Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'
ValueError: error processing: 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z
SES surface': Error while saving session data for 'named views' -> -> -> 'cap
near' -> '5mdv.pdb_z SES surface'
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in take_snapshot
data = {attr:getattr(self, attr) for attr in init_attrs}
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 577, in <dictcomp>
data = {attr:getattr(self, attr) for attr in init_attrs}
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 565, in get_color
return self._colors[0]
TypeError: 'NoneType' object is not subscriptable
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\ui\gui.py", line 1574, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 78, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface': Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x0000017A05370DC0> ->
<chimerax.std_commands.view.NamedView object at 0x0000017A05370F70> ->
<chimerax.surface.cap.ClipCap object at 0x0000017A14267490> 'cap near' ->
<chimerax.atomic.molsurf.MolecularSurface object at 0x0000017A7D287310>
'5mdv.pdb_z SES surface'
ValueError: error processing: 'named views' -> -> -> 'cap near' -> '5mdv.pdb_z
SES surface': Error while saving session data for 'named views' -> -> -> 'cap
near' -> '5mdv.pdb_z SES surface'
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 26.20.100.7870
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 81Q8
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 16,926,306,304
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
OSLanguage: de-DE
Locale: ('de_DE', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.11.8
cftime: 1.2.1
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.9.3
ChimeraX-AtomicLibrary: 1.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202011140750
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.1
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.3.1
ChimeraX-PDB: 2.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.2.2
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.3.1
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.6.3
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.5.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
netifaces: 0.10.9
networkx: 2.5
numexpr: 2.7.1
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.2.3
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.8
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.1
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.1
python-dateutil: 2.8.1
pytz: 2020.4
pywin32: 228
pyzmq: 20.0.0
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.0
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.35.1
WMI: 1.5.1
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