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Opened 5 years ago
Last modified 5 years ago
#4074 closed defect
ValueError after closing one session and opening another — at Version 1
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Thanks for the swift reply to my last report! I couldn't figure out how to reply to you, so I am re-reporting the issue after having the same results in ChimeraX 1.1 as in ChimeraX 0.93 and not 1.1. I'm getting these error messages when I try to File->Close Session and then re-open a new session (.cxs file) without closing ChimeraX 1.1 and they seem to relate to the alignment.py file in the seqalign folder. I did recently try some "align" commands, but I am not sure what I might have messed up. Oddly, when I restart ChimeraX 1.1, I have no trouble opening these same .cxs files. The error I get when I close a session is:
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
The error I get when I try to reopen a new session is:
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py", line 649, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session
Log from Sat Dec 12 22:38:48 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\ProgramData\ChimeraX\cpSRP43_NMR.cxs format session
Log from Sat Dec 12 13:41:49 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_PRE.cxs" format session
Log from Sun Nov 15 22:59:07 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session
Log from Fri Sep 18 14:58:13 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs format session
Log from Sun Aug 30 16:37:13 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43 structures\200812 cpSRP43
> FL CD2 labels.cxs" format session
Log from Wed Aug 12 13:28:02 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812 cpSRP43
> FL CD2 labels.cxs"
Log from Wed Aug 12 11:30:26 2020UCSF ChimeraX version: 0.93 (2020-03-24)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\Alex\Desktop\Zoom call.cxs" format session
File not found: C:\Users\Alex\Desktop\Zoom call.cxs
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_composite.pdb"
Summary of feedback from opening C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
structures/cpSRP43_composite.pdb
---
warning | Ignored bad PDB record found on line 2610
END
Chain information for cpSRP43_composite.pdb #1
---
Chain | Description
A | No description available
B | No description available
F | No description available
G | No description available
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_BTFA.py"
ChimeraX cannot open a regular Chimera session.
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.
> open "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_alone.pdb"
Summary of feedback from opening C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
structures/cpSRP43_alone.pdb
---
warnings | Ignored bad PDB record found on line 2938
END
Start residue of secondary structure not found: HELIX 1 1 SER A 117 TYR A 119
1 3
Start residue of secondary structure not found: HELIX 2 2 ALA A 122 LYS A 138
1 17
Start residue of secondary structure not found: HELIX 3 3 GLU A 141 GLN A 146
1 6
Start residue of secondary structure not found: HELIX 4 4 ALA A 163 LEU A 170
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP A 173 GLU A 181
1 9
47 messages similar to the above omitted
cpSRP43_alone.pdb title:
Crystal structure of the CPSRP54 tail bound to CPSRP43 [more info...]
Chain information for cpSRP43_alone.pdb
---
Chain | Description
2.1/A | signal recognition particle 43 kda protein, chloroplastic
2.4/B | signal recognition particle 54 kda protein, chloroplastic
2.5/B | signal recognition particle 54 kda protein, chloroplastic
2.2/C | No description available
2.3/E | No description available
> close session
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_alone.pdb"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_alone.pdb
---
warnings | Ignored bad PDB record found on line 2938
END
Start residue of secondary structure not found: HELIX 1 1 SER A 117 TYR A 119
1 3
Start residue of secondary structure not found: HELIX 2 2 ALA A 122 LYS A 138
1 17
Start residue of secondary structure not found: HELIX 3 3 GLU A 141 GLN A 146
1 6
Start residue of secondary structure not found: HELIX 4 4 ALA A 163 LEU A 170
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP A 173 GLU A 181
1 9
47 messages similar to the above omitted
cpSRP43_alone.pdb title:
Crystal structure of the CPSRP54 tail bound to CPSRP43 [more info...]
Chain information for cpSRP43_alone.pdb
---
Chain | Description
1.1/A | signal recognition particle 43 kda protein, chloroplastic
1.4/B | signal recognition particle 54 kda protein, chloroplastic
1.5/B | signal recognition particle 54 kda protein, chloroplastic
1.2/C | No description available
1.3/E | No description available
> set bgColor white
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"
> select clear
> close session
> open "C:\Users\Alex\Desktop\Zoom call.cxs" format session
File not found: C:\Users\Alex\Desktop\Zoom call.cxs
> open "C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
> structures\cpSRP43_NMRnum.pdb"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_NMRnum.pdb
---
warning | Ignored bad PDB record found on line 2498
END
Chain information for cpSRP43_NMRnum.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Alignment identifier is 1.A
Alignment identifier is 1.B
Alignment identifier is 1.C
Alignment identifier is 1.D
> select clear
> color lightgray
> select clear
> select clear
> select clear
> select clear
> show sel cartoons
> hide sel atoms
> color sel green
> show sel cartoons
> hide sel atoms
> color sel purple
> color sel red
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"
> select clear
> select /A:267
9 atoms, 8 bonds, 1 model selected
> select up
67 atoms, 67 bonds, 1 model selected
> select up
2227 atoms, 2266 bonds, 1 model selected
> hide sel atoms
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL.cxs"
> select clear
> select clear
> show sel atoms
> color sel black
> style sel ball
Changed 64 atom styles
> style sel sphere
Changed 64 atom styles
> style sel sphere
Changed 70 atom styles
> show sel atoms
> color sel black
> hbonds sel
9 hydrogen bonds found
> hbonds sel
9 hydrogen bonds found
> select clear
> toolshed show H-Bonds
> hbonds
249 hydrogen bonds found
> style sel stick
Changed 70 atom styles
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
> style sel stick
Changed 8 atom styles
> color sel black
> show sel atoms
> :145
Unknown command: :145
> select :145
11 atoms, 10 bonds, 1 model selected
> select :145,146
19 atoms, 18 bonds, 1 model selected
> select :145,146+2
Expected an objects specifier or a keyword
> select :145,146
19 atoms, 18 bonds, 1 model selected
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel ladder
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select clear
> toolshed show "Blast Protein"
> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service1597256347514386636114
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1597256347514386636114
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
> style stick
Changed 2494 atom styles
> color bynucleotide
> graphics silhouettes true
> toolshed show "Side View"
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> graphics silhouettes true
> lighting flat
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting simple
> ui mousemode rightMode "mark maximum"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode select
> ui mousemode rightMode select
Drag select of 2 residues, 1 pseudobonds
Drag select of 10 residues
> select clear
> ui mousemode rightMode pivot
> ui mousemode rightMode pivot
> ui mousemode rightMode "translate selected atoms"
> ui mousemode rightMode "translate selected atoms"
> ui mousemode rightMode translate
> ui mousemode rightMode rotate
> ui mousemode rightMode select
> select clear
> select /A:44
9 atoms, 8 bonds, 1 model selected
> select /A:43
8 atoms, 7 bonds, 1 model selected
> select /A:61
9 atoms, 8 bonds, 1 model selected
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
> toolshed show Toolbar
> toolshed show "Basic Actions"
> hide /A target abp
> hide /A target abp
> show /A target abp
> hide /A target abp
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> show sel atoms
> style sel stick
Changed 78 atom styles
> style sel stick
Changed 78 atom styles
> hide sel atoms
> style sel stick
Changed 78 atom styles
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 78 atom styles
> style sel sphere
Changed 78 atom styles
> style sel stick
Changed 78 atom styles
> show /A target abp
> hide sel atoms
> show sel atoms
> select clear
> hide atoms
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> show sel atoms
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
opened ChimeraX session
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color /A #ff11b8 target abp
> color /A #58fffa target abp
> color /A #cf3cff target abp
> show /A target c
> color /A #ffffff target c
> ui mousemode rightMode select
> ui mousemode rightMode pivot
> ui mousemode rightMode select
> ~hbonds
> hbonds
249 hydrogen bonds found
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> name frozen "single cys" sel
registering illegal selector name "single cys"
> select clear
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete
self.session.tools.remove([self])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
KeyError: 7
KeyError: 7
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete
self.session.tools.remove([self])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
KeyError: 8
KeyError: 8
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1901, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 588, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 496, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 176, in delete
self.session.tools.remove([self])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
KeyError: 9
KeyError: 9
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 360, in remove
del self._tool_instances[tid]
See log for complete Python traceback.
> select :209,216,230,234,239,246,253,257,267
78 atoms, 69 bonds, 2 pseudobonds, 2 models selected
> name frozen "single cys" sel
registering illegal selector name "single cys"
> name frozen "single cys" sel
registering illegal selector name "single cys"
> name frozen "single cys" sel
registering illegal selector name "single cys"
> name frozen singlecys sel
> name frozen singlecys sel
> color singlecys #ff3030 target abp
> color singlecys #00ff3b target abp
> select clear
> select /A:274
9 atoms, 8 bonds, 1 model selected
> select clear
Drag select of 1 atoms, 5 residues, 1 bonds
> select clear
> select /A:246
11 atoms, 10 bonds, 1 model selected
> select /A:253
6 atoms, 5 bonds, 1 model selected
> select /A:234
9 atoms, 8 bonds, 1 model selected
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43 structures/200812
> cpSRP43 FL CD2 labels.cxs"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\200812 cpSRP43 FL CD2 labels.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs
> select /A:213
9 atoms, 8 bonds, 1 model selected
> select up
142 atoms, 142 bonds, 1 model selected
> select up
2227 atoms, 2266 bonds, 1 model selected
> hide sel atoms
> ~hbonds
> select clear
> select :209,216,234,239,253,267
49 atoms, 43 bonds, 1 model selected
> show sel atoms
> select clear
> save C:\Users\Alex\Desktop\image2.png supersample 3
> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs
Summary of feedback from opening C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> save C:\Users\Alex\Desktop\image4.png supersample 3
> select :260,257,239,219,212,188,192
64 atoms, 58 bonds, 1 model selected
> select clear
> select :209,216,234,239,253,267
49 atoms, 43 bonds, 1 model selected
> label sel residues
> label sel residues size 96
> label sel residues font-size 96
Expected a keyword
> label sel residues 96
Expected a keyword
> label sel residues
> label sel residues 10
Expected a keyword
> label sel residues height 10
> label sel residues height 2
> select clear
> save session C:/Users/Alex/Desktop/cpSRP43-CD2-BTFMA.cxs
Summary of feedback from opening C:\Users\Alex\Desktop\cpSRP43-CD2-BTFMA.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> close #1.1
> select /A:213
9 atoms, 8 bonds, 1 model selected
> select up
142 atoms, 142 bonds, 1 model selected
> select up
2227 atoms, 2266 bonds, 1 model selected
> hide sel atoms
> select clear
> :90
Unknown command: :90
> select :46
8 atoms, 7 bonds, 1 model selected
> select :46,60,71,76,131,148,161,209,222
81 atoms, 72 bonds, 1 model selected
> style sel sphere
Changed 81 atom styles
> show sel cartoons
> show sel atoms
> style sel stick
Changed 81 atom styles
> select :46.CA,60,71,76,131,148,161,209,222
Expected an objects specifier or a keyword
> select :46@CA,60,71,76,131,148,161,209,222
1 atom, 1 model selected
> select :46@CA,60@CA,71@CA,76@CA,131@CA,148@CA,161@CA,20@CA9,222@CA
1 atom, 1 model selected
> hide sel atoms
> select CA :46,60,71,76,131,148,161,209,222
Expected an objects specifier or a keyword
> select @CA :46,60,71,76,131,148,161,209,222
390 atoms, 72 bonds, 1 model selected
> select :46,60,71,76,131,148,161,209,222@CA
10 atoms, 1 model selected
> style sel sphere
Changed 10 atom styles
> show sel atoms
> show sel atoms
> style sel sphere
Changed 10 atom styles
> select :46,60,71,76,131,148,161,209,222
81 atoms, 72 bonds, 1 model selected
> select :46,60,71,76,131,148,161,209,222@CA
10 atoms, 1 model selected
> show sel atoms
> style sel sphere
Changed 10 atom styles
> show sel atoms
> show sel cartoons
> style sel sphere
Changed 10 atom styles
> style sel stick
Changed 10 atom styles
> select #1:46,60,71,76,131,148,161,209,222@CA
10 atoms, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel black
> select #1.A:46,60,71,76,131,148,161,209,222@CA
Expected an objects specifier or a keyword
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> style sel sphere
Changed 9 atom styles
> hide sel cartoons
> select clear
> color lightgray,a;~display;color #A1FF00,a :90@CA1;display :90@CA1;color
> #1BFF00,a :104@CA1;display :104@CA1;color #FF0000,a :115@CA1;display
> :115@CA1;color #FF4600,a :120@CA1;display :120@CA1;color #FFCA00,a
> :175@CA1;display :175@CA1;color #00FF00,a :192@CA1;display :192@CA1;color
> #94FF00,a :205@CA1;display :205@CA1;color #44FF00,a :253@CA1;display
> :253@CA1;color #45FF00,a :266@CA1;display :266@CA1;~display
> #4.2;~ribbackbone;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color lightgray,a; ~display;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #A1FF00,a :90@CA1; display :90@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1BFF00,a :104@CA1; display :104@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #FF0000,a :115@CA1; display :115@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #FF4600,a :120@CA1; display :120@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #FFCA00,a :175@CA1; display :175@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #00FF00,a :192@CA1; display :192@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #94FF00,a :205@CA1; display :205@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #44FF00,a :253@CA1; display :253@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #45FF00,a :266@CA1; display :266@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #A1FF00,a :90@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> hide sel cartoons
> color #A1FF00 /A:90@CA1;
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #A1FF00 :90@CA;
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select /A:46
8 atoms, 7 bonds, 1 model selected
> color #A1FF00,a :46@CA1;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #A1FF00,a :46@CA;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select :46@CA
1 atom, 1 model selected
> color sel #A1FF00
> color lightgray,a;sel /A:46@CA;color sel #A1FF00,a :46@CA;sel /A:60@CA;color
> sel #1BFF00,a :60@CA;sel /A:71@CA;color sel #FF0000,a :71@CA;sel
> /A:76@CA;color sel #FF4600,a :76@CA;sel /A:131@CA;color sel #FFCA00,a
> :131@CA;sel /A:148@CA;color sel #00FF00,a :148@CA;sel /A:161@CA;color sel
> #94FF00,a :161@CA;sel /A:209@CA;color sel #44FF00,a :209@CA;sel
> /A:222@CA;color sel #45FF00,a :222@CA;~display #4.2;~ribbackbone;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select /A:46@CA
1 atom, 1 model selected
> color sel #A1FF00,a :46@CA;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color lightgray,a;sel /A:46@CA;color sel #A1FF00;sel /A:60@CA;color sel
> #1BFF00;sel /A:71@CA;color sel #FF0000;sel /A:76@CA;color sel #FF4600;sel
> /A:131@CA;color sel #FFCA00;sel /A:148@CA;color sel #00FF00;sel
> /A:161@CA;color sel #94FF00;sel /A:209@CA;color sel #44FF00;sel
> /A:222@CA;color sel #45FF00;~display #4.2;~ribbackbone;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel #A1FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #1BFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:76@CA
1 atom, 1 model selected
> color sel #FF4600
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFCA00
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #94FF00
> select /A:209@CA
1 atom, 1 model selected
> color sel #44FF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #45FF00
> select clear
> select /A:46@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #8AFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #94FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFA000
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FFDC00
> select /A:209@CA
1 atom, 1 model selected
> color sel #CAFF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #FFBC00
> vdwdefine 2.0
Unknown command: vdwdefine 2.0
> vdw 2.0
Unknown command: vdw 2.0
> ballScale 0.5
Unknown command: ballScale 0.5
> ballScale
Unknown command: ballScale
> size ballScale 0.5
Changed 1 ball scales
> size ballScale 1
Changed 1 ball scales
> select clear
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> size ballScale 1
Changed 1 ball scales
> size atomRadius 1
Changed 2494 atom radii
> size atomRadius 5
Changed 2494 atom radii
> size atomRadius 2
Changed 2494 atom radii
> size atomRadius 3
Changed 2494 atom radii
> select clear
> save C:\Users\Alex\Desktop\image9.png supersample 3
> save C:\Users\Alex\Desktop\image10.png supersample 3
> select /A:46@CA
1 atom, 1 model selected
> color sel #99FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #5EFF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #5AFF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFD700
> select /A:148@CA
1 atom, 1 model selected
> color sel #3DFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF2100
> select /A:209@CA
1 atom, 1 model selected
> color sel #FFB500
> select /A:222@CA
1 atom, 1 model selected
> color sel #FFE400
> select /A:46@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #5CFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #62FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #EAFF00
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #C2FF00
> select /A:209@CA
1 atom, 1 model selected
> color sel #86FF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #D7FF00
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select clear
> save C:\Users\Alex\Desktop\image10.png supersample 3
> select /A:46,60,71,75,131,148,161,209,222@CA
9 atoms, 1 model selected
> hide sel cartoons
> style sel sphere
Changed 9 atom styles
> show sel atoms
> select /A:76@CA
1 atom, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select /A:76
8 atoms, 7 bonds, 1 model selected
> color sel lightgray
> select clear
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:76@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:75@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select clear
> save C:\Users\Alex\Desktop\image11.png supersample 3
> select /A:46@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #8AFF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:75@CA
1 atom, 1 model selected
> color sel #94FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FFA000
> select /A:148@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FFDC00
> select /A:209@CA
1 atom, 1 model selected
> color sel #CAFF00
> select /A:222@CA
1 atom, 1 model selected
> color sel #FFBC00
> save C:\Users\Alex\Desktop\image12.png supersample 3
> select clear
> save C:\Users\Alex\Desktop\image13.png supersample 3
> select /A:46@CA
1 atom, 1 model selected
> color sel #E5FF00
> select /A:60@CA
1 atom, 1 model selected
> color sel #00FF00
> select /A:71@CA
1 atom, 1 model selected
> color sel #8DFF00
> select /A:75@CA
1 atom, 1 model selected
> color sel #87FF00
> select /A:131@CA
1 atom, 1 model selected
> color sel #FF4300
> select /A:148@CA
1 atom, 1 model selected
> color sel #5BFF00
> select /A:161@CA
1 atom, 1 model selected
> color sel #FF0000
> select /A:209@CA
1 atom, 1 model selected
> color sel #FF1000
> select /A:220@CA
1 atom, 1 model selected
> color sel #FF5600
> select /A:220@CA
1 atom, 1 model selected
> hide sel cartoons
> select /A:220@CA
1 atom, 1 model selected
> select /A:220@CA
1 atom, 1 model selected
> hide sel cartoons
> style sel sphere
Changed 1 atom style
> select clear
> save C:\Users\Alex\Desktop\image14.png supersample 3
> select /A:222@CA
1 atom, 1 model selected
> color sel #FF5600
> select clear
> save C:\Users\Alex\Desktop\image15.png supersample 3
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select /A:220@CA
1 atom, 1 model selected
> show sel atoms
> select /A:222@CA
1 atom, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> color sel lightgray
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_EPR.cxs"
> select clear
> select :240
8 atoms, 7 bonds, 1 model selected
> select :240,242
17 atoms, 15 bonds, 1 model selected
> select clear
> hide atoms
> show cartoons
> color lightgray
> select /A:46,60,71,76,131,148,161,209,222@CA
9 atoms, 1 model selected
> color sel lightgray
> select /A:220
4 atoms, 3 bonds, 1 model selected
> color sel lightgray
> select clear
> select /A:75
12 atoms, 12 bonds, 1 model selected
> color sel lightgray
> select clear
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_PRE.cxs"
> select clear
> select :240,242
17 atoms, 15 bonds, 1 model selected
> show sel atoms
> color sel lightgray
> select clear
> select /A:242@OE2
1 atom, 1 model selected
> select /A:242
9 atoms, 8 bonds, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 model selected
> select clear
> toolshed show "Build Structure"
> swapaa :240 CYS
Using Dunbrack library
/A ASP 240: phi -80.0, psi 25.3 trans
Applying CYS rotamer (chi angles: -177.4) to /A CYS 240
> swapaa :242 CYS
Using Dunbrack library
/A GLU 242: phi -114.6, psi 124.4 trans
Applying CYS rotamer (chi angles: -61.6) to /A CYS 242
> select /A:242@SG
1 atom, 1 model selected
> style sel sphere
Changed 2 atom styles
> color sel red
> select /A:242@SG
1 atom, 1 model selected
> color :240@S red
> color :240@CS red
> color :240@SH red
> color :240@SG red
> color :242@SG red
> select clear
> select /A:242@SG
1 atom, 1 model selected
> select /A:213
9 atoms, 8 bonds, 1 model selected
> select clear
> select /A:242
6 atoms, 5 bonds, 1 model selected
> color :242@CA lightgray
> color :240@CA lightgray
> select clear
> select :ile
88 atoms, 78 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 88 atom styles
> color sel lightgray
> select :ile@CG
Nothing selected
> select :ile@CD
Nothing selected
> select :ile@CG1
11 atoms, 1 model selected
> style sel sphere
Changed 11 atom styles
> select down
11 atoms, 1 model selected
> select up
88 atoms, 78 bonds, 1 model selected
> select up
559 atoms, 558 bonds, 1 model selected
> select up
2222 atoms, 2261 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select up
2489 atoms, 2531 bonds, 1 model selected
> select down
2222 atoms, 2261 bonds, 1 model selected
> select down
559 atoms, 558 bonds, 1 model selected
> select down
88 atoms, 78 bonds, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> select down
11 atoms, 1 model selected
> size sphereRadius 2
Expected a keyword
> size sphereRadius
Expected a keyword
> size radius 2
Expected a keyword
> size atomRadius 2
Changed 2489 atom radii
> select clear
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select :ile@CG1
11 atoms, 1 model selected
> color sel black
> select :ile@CA
11 atoms, 1 model selected
> color sel lightgray
> select clear
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select :leu@CD1
28 atoms, 1 model selected
> select clear
> select /A:242@SG
1 atom, 1 model selected
> toolshed show Distances
> distance /A:209@CG1 /A:242@SG
Distance between /A ILE 209 CG1 and CYS 242 SG: 28.782Å
> distance style color red
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style decimalPlaces 1
> distance style decimalPlaces 0
> distance style decimalPlaces 0
> distance style radius 0.11
> distance style radius 0.11
> distance style radius 0.12
> distance style radius 0.12
> distance style radius 0.13
> distance style radius 0.13
> distance style radius 0.14
> distance style radius 0.14
> distance style radius 0.15
> distance style radius 0.15
> distance style radius 0.16
> distance style radius 0.16
> distance style radius 0.17
> distance style radius 0.17
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.19
> distance style radius 0.19
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.17
> distance style radius 0.17
> distance style radius 0.16
> distance style radius 0.16
> distance style radius 0.15
> distance style radius 0.15
> distance style radius 0.14
> distance style radius 0.14
> distance style radius 0.13
> distance style radius 0.13
> distance style radius 0.12
> distance style radius 0.12
> distance style radius 0.11
> distance style radius 0.11
> distance style radius 0.1
> distance style radius 0.1
> select /A:242@SG
1 atom, 1 model selected
> distance /A:215@CG1 /A:242@SG
Distance between /A ILE 215 CG1 and CYS 242 SG: 22Å
> select /A:242@SG
1 atom, 1 model selected
> select clear
> select /A:242@SG
1 atom, 1 model selected
> distance /A:176@CG1 /A:242@SG
Distance between /A ILE 176 CG1 and CYS 242 SG: 25Å
Must select one or more distances in the table
> ~distance /A:176@CG1 /A:242@SG
> ~distance /A:209@CG1 /A:242@SG
> ~distance /A:215@CG1 /A:242@SG
> select /A:240@SG
1 atom, 1 model selected
> distance /A:176@CG1 /A:240@SG
Distance between /A ILE 176 CG1 and CYS 240 SG: 27Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:215@CG1 /A:240@SG
Distance between /A ILE 215 CG1 and CYS 240 SG: 22Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:209@CG1 /A:240@SG
Distance between /A ILE 209 CG1 and CYS 240 SG: 27Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:193@CG1 /A:240@SG
Distance between /A ILE 193 CG1 and CYS 240 SG: 27Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:231@CG1 /A:240@SG
Distance between /A ILE 231 CG1 and CYS 240 SG: 15Å
> select clear
> select /A:240@SG
1 atom, 1 model selected
> distance /A:293@CG1 /A:240@SG
Distance between /A ILE 293 CG1 and CYS 240 SG: 41Å
> select clear
> ~distance /A:215@CG1 /A:240@SG
> undo
> select /A:215@CG1
1 atom, 1 model selected
> distance /A:215@CG1 /A:240@SG
Distance between /A ILE 215 CG1 and CYS 240 SG: 22Å
> select clear
> ~distance /A:293@CG1 /A:240@SG
> select clear
> 2dlabels size 12
> 2dlabels size 24
> label size 24
> label size 48
> select clear
> save C:\Users\Alex\Desktop\image16.png supersample 3
> select clear
> select /D:536
11 atoms, 10 bonds, 1 model selected
> select up
43 atoms, 42 bonds, 1 model selected
> select up
104 atoms, 105 bonds, 1 model selected
> hide sel cartoons
> select clear
> select /A:225
12 atoms, 12 bonds, 1 model selected
> select /A:285
11 atoms, 10 bonds, 1 model selected
> select up
31 atoms, 30 bonds, 1 model selected
> select up
2222 atoms, 2261 bonds, 1 model selected
> select down
31 atoms, 30 bonds, 1 model selected
> select down
11 atoms, 10 bonds, 1 model selected
> select down
11 atoms, 10 bonds, 1 model selected
Destroying pre-existing alignment with identifier 1.A
Alignment identifier is 1.A
> select clear
> select /A:223
11 atoms, 11 bonds, 1 model selected
> hide sel cartoons
> show sel atoms
> toolshed show Rotamers
> save session "C:/Users/Alex/Google Drive/Shan Lab/cpSRP43
> structures/cpSRP43_PRE.cxs"
Summary of feedback from opening C:\Users\Alex\Google Drive\Shan Lab\cpSRP43
structures\cpSRP43_PRE.cxs
---
warning | registering illegal selector name "single cys"
opened ChimeraX session
> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs
> select clear
> hide target a
> select clear
> select /A:224
9 atoms, 8 bonds, 1 model selected
> select up
46 atoms, 47 bonds, 1 model selected
> select up
2222 atoms, 2261 bonds, 1 model selected
> show sel cartoons
> select clear
> show cartoons
> select clear
> select /A:240
6 atoms, 5 bonds, 1 model selected
> select :240@S
Nothing selected
> select :240.S
Expected an objects specifier or a keyword
> select :240@SH
Nothing selected
> select :240@sh
Nothing selected
> select :240@s
Nothing selected
> select :240@c
1 atom, 1 model selected
> select :240@ca
1 atom, 1 model selected
> select :240@cb
1 atom, 1 model selected
> select :240@sh
Nothing selected
> select /A:240
6 atoms, 5 bonds, 1 model selected
> show sel atoms
> select /A:240@SG
1 atom, 1 model selected
> color sel black
> select clear
> select clear
> select /A:240@SG
1 atom, 1 model selected
> color sel lightgray
> select :240@sg
1 atom, 1 model selected
> select clear
> select :240@sg
1 atom, 1 model selected
> color sel black
> ribbackbone
Unknown command: ribbackbone
> select clear
> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs
> select /A:240
6 atoms, 5 bonds, 1 model selected
> color sel lightgray
> color :240 at SG black
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black, :240 at SG
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black, :240@sg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black,a :240@sg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black,a :240.a@sg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color black :240.a@sg
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color black :240@sg
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select /A:240@SG
1 atom, 1 model selected
> color black :240@sg
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
[had to nuke a large part of the log in order to fit in ticket]
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> ~display /B
> select /A:239@N
1 atom, 1 model selected
> hide sel atoms
> select clear
> view fron
Expected an objects specifier or a view name or a keyword
> view front
> select /A:44@N
1 atom, 1 model selected
> hide sel atoms
> select clear
> view back
> save C:\Users\Alex\Desktop\image26.png supersample 3
> view front
> save C:\Users\Alex\Desktop\image27.png supersample 3
> select clear
> view back
> save C:\Users\Alex\Desktop\image28.png supersample 3
> color /A lightgray
> cartoon suppressBackboneDisplay false
> ~display
> color :240@n,a black target a
> display :240@n
> color :15@CG1,a #00FF00 target a
> display :15@CG1
> color :26@CG1,a #B3FF00 target a
> display :26@CG1
> color :26@CG2,a #00FF00 target a
> display :26@CG2
> color :42@CG1,a #00FF00 target a
> display :42@CG1
> color :42@CG2,a #FF0000 target a
> display :42@CG2
> color :45@CD1,a #00FF00 target a
> display :45@CD1
> color :59@CD1,a #00FF00 target a
> display :59@CD1
> color :59@CD2,a #FF1F00 target a
> display :59@CD2
> color :60@CD1,a #61FF00 target a
> display :60@CD1
> color :71@CG1,a #FFBC00 target a
> display :71@CG1
> color :80@CG1,a #17FF00 target a
> display :80@CG1
> color :81@CG1,a #FF0000 target a
> display :81@CG1
> color :109@CG1,a #FF0000 target a
> display :109@CG1
> color :112@CG1,a #FF0000 target a
> display :112@CG1
> color :134@CD1,a #FF0000 target a
> display :134@CD1
> color :142@CD1,a #00FF00 target a
> display :142@CD1
> color :142@CD2,a #FF0000 target a
> display :142@CD2
> color :209@CD1,a #FF0000 target a
> display :209@CD1
> color :211@CD1,a #FF0000 target a
> display :211@CD1
> color :215@CD1,a #FF0000 target a
> display :215@CD1
> color :217@CG1,a #FF0000 target a
> display :217@CG1
> color :277@CG1,a #FFD600 target a
> display :277@CG1
> color :281@CG1,a #00FF00 target a
> display :281@CG1
> color :281@CG2,a #00FF00 target a
> display :281@CG2
> color :282@CD1,a #00FF00 target a
> display :282@CD1
> color :286@CG1,a #00FF00 target a
> display :286@CG1
> color :286@CG2,a #00FF00 target a
> display :286@CG2
> color :293@CD1,a #00FF00 target a
> display :293@CD1
> color :296@CD1,a #00FF00 target a
> display :296@CD1
> color :297@CG1,a #00FF00 target a
> display :297@CG1
> color :297@CG2,a #00FF00 target a
> display :297@CG2
> color :313@CG1,a #00FF00 target a
> display :313@CG1
> color :317@CD1,a #FFD700 target a
> display :317@CD1
> color :317@CD2,a #CBFF00 target a
> display :317@CD2
> color :318@CG1,a #00FF00 target a
> display :318@CG1
> color :319@CD1,a #FF0000 target a
> display :319@CD1
> color :319@CD2,a #FF0000 target a
> display :319@CD2
> color :320@CD1,a #FF1B00 target a
> display :320@CD1
> color :0@1,a #FF0000 target a
> display :0@1
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> color :0@2,a #FF0000 target a
> display :0@2
> ~display /B
> hide sel atoms
> select clear
> view back
> view front
> save C:\Users\Alex\Desktop\image25.png supersample 3
> view front
> view front
> color :3@N,a #FF4900 target a
> display :3@N
> color :4@N,a #FF0000 target a
> display :4@N
> color :12@N,a #FFAA00 target a
> display :12@N
> color :13@N,a #FFB500 target a
> display :13@N
> color :14@N,a #FF9D00 target a
> display :14@N
> color :17@N,a #FFFA00 target a
> display :17@N
> color :19@N,a #FFB500 target a
> display :19@N
> color :20@N,a #FFF600 target a
> display :20@N
> color :22@N,a #A2FF00 target a
> display :22@N
> color :23@N,a #6AFF00 target a
> display :23@N
> color :26@N,a #42FF00 target a
> display :26@N
> color :27@N,a #00FF00 target a
> display :27@N
> color :28@N,a #E9FF00 target a
> display :28@N
> color :29@N,a #00FF00 target a
> display :29@N
> color :30@N,a #25FF00 target a
> display :30@N
> color :31@N,a #2DFF00 target a
> display :31@N
> color :32@N,a #87FF00 target a
> display :32@N
> color :33@N,a #44FF00 target a
> display :33@N
> color :34@N,a #52FF00 target a
> display :34@N
> color :36@N,a #8CFF00 target a
> display :36@N
> color :37@N,a #FF0000 target a
> display :37@N
> color :39@N,a #FF7000 target a
> display :39@N
> color :44@N,a #FF0000 target a
> display :44@N
> color :54@N,a #FFBB00 target a
> display :54@N
> color :74@N,a #FFB800 target a
> display :74@N
> color :128@N,a #FF6F00 target a
> display :128@N
> color :140@N,a #FF3C00 target a
> display :140@N
> color :150@N,a #FFF800 target a
> display :150@N
> color :156@N,a #FF6700 target a
> display :156@N
> color :157@N,a #FF4C00 target a
> display :157@N
> color :169@N,a #FFED00 target a
> display :169@N
> color :177@N,a #FFC700 target a
> display :177@N
> color :188@N,a #FFA400 target a
> display :188@N
> color :189@N,a #FF0000 target a
> display :189@N
> color :190@N,a #FFBA00 target a
> display :190@N
> color :191@N,a #FF3C00 target a
> display :191@N
> color :192@N,a #FF0000 target a
> display :192@N
> color :239@N,a #FFF300 target a
> display :239@N
> color :274@N,a #FF7400 target a
> display :274@N
> color :281@N,a #FFA900 target a
> display :281@N
> color :282@N,a #4CFF00 target a
> display :282@N
> color :283@N,a #5AFF00 target a
> display :283@N
> color :284@N,a #D8FF00 target a
> display :284@N
> color :285@N,a #05FF00 target a
> display :285@N
> color :286@N,a #AFFF00 target a
> display :286@N
> color :287@N,a #0EFF00 target a
> display :287@N
> color :288@N,a #FFEA00 target a
> display :288@N
> color :289@N,a #E4FF00 target a
> display :289@N
> color :290@N,a #35FF00 target a
> display :290@N
> color :292@N,a #5FFF00 target a
> display :292@N
> color :293@N,a #22FF00 target a
> display :293@N
> color :294@N,a #2FFF00 target a
> display :294@N
> color :295@N,a #00FF00 target a
> display :295@N
> color :296@N,a #14FF00 target a
> display :296@N
> color :297@N,a #18FF00 target a
> display :297@N
> color :298@N,a #6AFF00 target a
> display :298@N
> color :304@N,a #FFD000 target a
> display :304@N
> color :305@N,a #FF0000 target a
> display :305@N
> color :306@N,a #AAFF00 target a
> display :306@N
> color :307@N,a #FF9E00 target a
> display :307@N
> color :310@N,a #65FF00 target a
> display :310@N
> color :313@N,a #FFCB00 target a
> display :313@N
> color :314@N,a #FF9E00 target a
> display :314@N
> color :315@N,a #FF6600 target a
> display :315@N
> color :316@N,a #FFDB00 target a
> display :316@N
> color :317@N,a #E3FF00 target a
> display :317@N
> color :318@N,a #5AFF00 target a
> display :318@N
> color :319@N,a #C6FF00 target a
> display :319@N
> color :320@N,a #9CFF00 target a
> display :320@N
> color :321@N,a #3DFF00 target a
> display :321@N
> color :323@N,a #61FF00 target a
> display :323@N
> color :324@N,a #00FF00 target a
> display :324@N
> color :325@N,a #35FF00 target a
> display :325@N
> color :327@N,a #77FF00 target a
> display :327@N
> color :328@N,a #38FF00 target a
> display :328@N
> color :329@N,a #00FF00 target a
> display :329@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
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> display :0@N
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> ~display /B
> hide sel atoms
> select clear
> save C:\Users\Alex\Desktop\image25.png supersample 3
> color /A lightgray
> cartoon suppressBackboneDisplay false
> ~display
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> ~display /B
> hide sel atoms
> color /A lightgray
> cartoon suppressBackboneDisplay false
> ~display
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> ~display /B
> select clear
> hide sel atoms
> view back
> hide sel atoms
> save C:\Users\Alex\Desktop\image25.png supersample 3
> view front
> save C:\Users\Alex\Desktop\image26.png supersample 3
> select clear
> select clear
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> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> color :0@N,a #FF0000 target a
> display :0@N
> ~display /B
> hide sel atoms
> hide sel atoms
> view front
> view back
> hide sel atoms
> hide sel atoms
> select clear
> hide sel atoms
> select clear
> save C:\Users\Alex\Desktop\image27.png supersample 3
> view front
> save C:\Users\Alex\Desktop\image28.png supersample 3
> hide sel atoms
> save C:\Users\Alex\Desktop\image29.png supersample 3
> select /A:209@CD1
1 atom, 1 model selected
> toolshed show Distances
> distance /A:142@N /A:209@CD1
Distance between /A LEU 142 N and ILE 209 CD1: 30.140Å
> view back
> select clear
> save session C:/ProgramData/ChimeraX/cpSRP43_PRE_colored.cxs
opened ChimeraX session
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 914, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 633, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 373, in detach_viewer
self.session.alignments.destroy_alignment(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment
del self._alignments[alignment.ident]
KeyError: '1.A'
KeyError: '1.A'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 107, in destroy_alignment
del self._alignments[alignment.ident]
See log for complete Python traceback.
> open C:\ProgramData\ChimeraX\cpSRP43_PRE_colored.cxs format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 649, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 649, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 629, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 440, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 456, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 691, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 292, in reset_state
tool_inst.delete()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
ValueError: list.remove(x): x not in list
ValueError: list.remove(x): x not in list
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 24.20.100.6293
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Book
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 17,101,541,376
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-6600U CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
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: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
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: 2.0
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: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
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: 1.2.3
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: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
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: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (1)
comment:1 by , 5 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → ValueError after closing one session and opening another |
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