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Opened 3 years ago
Last modified 3 years ago
#8840 assigned defect
Error when additional user joins meeting — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | VR | 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: macOS-12.6.4-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Another user in a meeting turned VR on and a bunch of errors kept scrolling and CHimeraX mostly froze for me. The VR session for the remote user kept working.
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_dd.cxs
> format session
Log from Thu Feb 2 11:36:33 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
Log from Thu Feb 2 10:34:00 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk.cxs
Log from Wed Feb 1 14:51:18 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
Log from Tue Jan 31 14:24:37 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Volumes/NO NAME/eNOS/enos_2Hb.cxs"
Log from Thu Jan 26 11:18:44 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.cxs
Log from Tue Jan 24 12:31:18 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> format session
Log from Fri Jun 24 15:04:01 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
Log from Fri Jun 24 13:21:50 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3.pdb"
Summary of feedback from opening /Users/cruzp2/OneDrive - National Institutes
of Health/eNOS_Hba/Steve_figure/cluster4_3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_162w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_162.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster4_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> ui tool show "Color Actions"
> color sel dark slate gray
> color sel midnight blue
> color sel salmon
> select #1/A:2000=2999
Expected an objects specifier or a keyword
> select #1/A:2000-2999
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel sienna
> select clear
> select ::name="HEM"
252 atoms, 264 bonds, 36 pseudobonds, 6 residues, 2 models selected
> color sel byelement
> select clear
> select #1/B:1000-1999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel forest green
> color sel sea green
> color sel medium sea green
> color sel medium spring green
> color sel light sea green
> select #1/B:3000-3999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel sea green
> color sel olive drab
> color sel chartreuse
> color sel medium aquamarine
> select #1/B:1000-1999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel cornflower blue
> select #1/B:3000-3999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel cyan
> color sel green
> color sel turquoise
> color sel dark turquoise
> color sel medium aquamarine
> color sel light green
> color sel sky blue
> select clear
> select #1/B:2000-2999
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> color sel medium aquamarine
> color sel cadet blue
> color sel teal
> color sel light sea green
> color sel turquoise
> color sel dark turquoise
> color sel lawn green
> color sel green yellow
> color sel pale green
> select #1/B:1-999
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> color sel light sea green
> color sel medium aquamarine
> color sel turquoise
> color sel medium turquoise
> select clear
> select ::name="HEM"
252 atoms, 264 bonds, 36 pseudobonds, 6 residues, 2 models selected
> color sel byelement
> select clear
> select #1/B:1004-1017
106 atoms, 108 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel pale violet red
> color sel medium orchid
> color sel orchid
> color sel violet
> color sel plum
[Repeated 1 time(s)]
> color sel violet
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> select #1/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> show sel surfaces
> close #1.2
> close #1.3
> select clear
> select #1/A
6540 atoms, 6723 bonds, 16 pseudobonds, 806 residues, 2 models selected
> surface sel
> close #1.2
> select clear
> select #1/A:2000-2999
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel light coral
> select clear
> select #1/A:2000-2999
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel light pink
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> select #1/B:3087-3097
89 atoms, 90 bonds, 11 residues, 1 model selected
> color sel midnight blue
> color sel hot pink
> color sel pale violet red
> color sel hot pink
> color sel dark violet
> color sel antique white
> color sel light pink
> color sel dark blue
> color sel navajo white
[Repeated 1 time(s)]
> color sel orchid
> color sel hot pink
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
10726 atoms, 11025 bonds, 1368 residues, 1 model selected
> hide sel atoms
> select clear
> select ::name="HEM"
252 atoms, 264 bonds, 36 pseudobonds, 6 residues, 2 models selected
> style sel ball
Changed 252 atom styles
> style sel sphere
Changed 252 atom styles
> select clear
> select #1/B:1117-1126
82 atoms, 86 bonds, 10 residues, 1 model selected
> color sel deep pink
> select #1/B:3087-3097
89 atoms, 90 bonds, 11 residues, 1 model selected
> color sel light pink
> color sel pale violet red
> color sel thistle
> color sel light coral
> color sel pale violet red
> color sel orchid
> color sel purple
> color sel medium purple
> color sel pale violet red
> color sel rebecca purple
> color sel pink
> color sel violet
> color sel lavender
> color sel powder blue
> color sel pale violet red
> select clear
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel coral
> select clear
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel dark salmon
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> help help:user
> select /A:432
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
143 atoms, 146 bonds, 18 residues, 1 model selected
> select up
2874 atoms, 2957 bonds, 359 residues, 1 model selected
> surface sel enclose sel
> select /A:2130
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> surface sel enclose sel
> select clear
> select add #1.2
2874 atoms, 359 residues, 1 model selected
> hide #1.2 models
> show #1.2 models
> color sel salmon target s
> select subtract #1.2
1 model selected
> select add #1.2
2874 atoms, 359 residues, 1 model selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> select add #1.3
6072 atoms, 759 residues, 2 models selected
> select subtract #1.2
3198 atoms, 400 residues, 3 models selected
> color sel sandy brown target s
> color sel light salmon target s
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> hide #1.2 models
> select clear
> select /A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 2 models selected
> select up
2874 atoms, 2957 bonds, 359 residues, 2 models selected
> select up
3053 atoms, 3140 bonds, 382 residues, 2 models selected
> select up
6396 atoms, 6579 bonds, 800 residues, 3 models selected
> select down
3053 atoms, 3140 bonds, 382 residues, 3 models selected
> select up
6396 atoms, 6579 bonds, 800 residues, 3 models selected
> select down
3053 atoms, 3140 bonds, 382 residues, 3 models selected
> select up
6396 atoms, 6579 bonds, 800 residues, 3 models selected
> select up
6540 atoms, 6723 bonds, 806 residues, 3 models selected
> select up
11038 atoms, 11345 bonds, 1378 residues, 3 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select #1/A:1-999
3270 atoms, 3361 bonds, 8 pseudobonds, 403 residues, 2 models selected
> surface sel enclose sel
> color sel salmon target s
> select clear
> select /A:2042
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2390@CB
1 atom, 1 residue, 1 model selected
> select /A:2041
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:2042
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2041
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:2041
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:2042
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2023@NE2
1 atom, 1 residue, 1 model selected
> select /A:439@CA
1 atom, 1 residue, 1 model selected
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
——— End of log from Fri Jun 24 13:21:50 2022 ———
opened ChimeraX session
> swapaa mousemode /A:139 MET
> swapaa mousemode /A:438 TRP
> swapaa mousemode /A:412 PRO
> swapaa mousemode /A:2310 PHE
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> help help:user
> swapaa mousemode /A:2015 TYR
> select /B:36
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:36-50
131 atoms, 138 bonds, 15 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:34-36
25 atoms, 25 bonds, 3 residues, 1 model selected
> select /B:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
swapaa cannot align to residues /B HEM 201 which has fewer than 3 backbone
atoms (N, C, CA)
> color sel red
> select clear
> swapaa mousemode /A:83 SER
> swapaa mousemode /A:68 PRO
> swapaa mousemode /A:435 TRP
> swapaa mousemode /A:84 VAL
> swapaa mousemode /A:81 GLY
[Repeated 1 time(s)]
> swapaa mousemode /A:70 GLY
> swapaa mousemode /A:140 LEU
> swapaa mousemode /A:439 MET
> swapaa mousemode /A:81 MET
> swapaa mousemode /A:79 ILE
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HAR"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
10746 atoms, 11044 bonds, 4 pseudobonds, 1370 residues, 2 models selected
> hide sel atoms
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
——— End of log from Fri Jun 24 15:04:01 2022 ———
opened ChimeraX session
> hide #1.2 models
> hide #1.3 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> close session
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_sym_copy.pdb
Summary of feedback from opening /Users/cruzp2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_sym_copy.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_162w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_162.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 SER A 85 GLN A 87 1
3
Start residue of secondary structure not found: HELIX 2 2 LEU A 123 SER A 137
1 15
Start residue of secondary structure not found: HELIX 3 3 GLN A 144 THR A 160
1 17
Start residue of secondary structure not found: HELIX 4 4 GLU A 167 ASN A 180
1 14
Start residue of secondary structure not found: HELIX 5 5 ALA A 204 GLY A 222
1 19
282 messages similar to the above omitted
End residue of secondary structure not found: HELIX 30 30 ALA B 53 ALA B 71 1
19
Start residue of secondary structure not found: HELIX 31 31 VAL B 73 ALA B 79
1 7
Start residue of secondary structure not found: HELIX 32 32 SER B 81 LYS B 90
1 10
Start residue of secondary structure not found: HELIX 33 33 PRO B 95 HIS B 112
1 18
Start residue of secondary structure not found: HELIX 34 34 PRO B 119 LEU B
136 1 18
Start residue of secondary structure not found: HELIX 35 35 PRO B 1005 LYS B
1017 1 13
80 messages similar to the above omitted
End residue of secondary structure not found: HELIX 30 30 ALA B 53 ALA B 71 1
19
Start residue of secondary structure not found: HELIX 31 31 VAL B 73 ALA B 79
1 7
Start residue of secondary structure not found: HELIX 32 32 SER B 81 LYS B 90
1 10
Start residue of secondary structure not found: HELIX 33 33 PRO B 95 HIS B 112
1 18
Start residue of secondary structure not found: HELIX 34 34 PRO B 119 LEU B
136 1 18
Start residue of secondary structure not found: HELIX 35 35 PRO B 1005 LYS B
1017 1 13
51 messages similar to the above omitted
Chain information for cluster4_3_sym_copy.pdb
---
Chain | Description
1.1/A 1.2/A 1.4/A 1.6/A | No description available
1.8/A 1.9/A | No description available
1.1/B 1.2/B 1.5/B 1.6/B | No description available
1.8/B 1.9/B | No description available
> hide #!1.9 models
> hide #!1.8 models
> hide #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> close session
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3.pdb_cluster4_3_sym_copy.pdb
Summary of feedback from opening /Users/cruzp2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3.pdb_cluster4_3_sym_copy.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_162w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_162.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster4_3.pdb_cluster4_3_sym_copy.pdb #1
---
Chain | Description
A | No description available
B | No description available
> help help:user
> combine #1 name enos_A
> combine #1 enos_B
Expected a keyword
> combine #1 name enos_B
> combine #1 name HB_A
> combine #1 name HB_B
> combine #1 name HB_C
> combine #1 name HB_D
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> select #2/B
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A:1000-2000
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!3 models
> hide #!2 models
> select #3/B
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #2/A:0-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #3/A:0-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show #!2 models
> combine #2-3 name enos_AB
Remapping chain ID 'A' in enos_B #3 to 'B'
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> close #8
> combine #2-3 name enos_AB
Remapping chain ID 'A' in enos_B #3 to 'B'
> hide #!2 models
> hide #!3 models
> hide #!8 models
> show #!2 models
> show #!3 models
> hide #!2 models
> close #8
> show #!2 models
> hide #!2 models
> ui tool show "Change Chain IDs"
> select add #3
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> show #!1 models
> hide #!3 models
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain
(cluster4_3.pdb_cluster4_3_sym_copy.pdb #1/A)
> select #1/B
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> ui tool show "Change Chain IDs"
> changechains sel Z
Chain IDs of 572 residues changed
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain
(cluster4_3.pdb_cluster4_3_sym_copy.pdb #1/A)
> select add #3
6540 atoms, 6724 bonds, 16 pseudobonds, 806 residues, 4 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain
(cluster4_3.pdb_cluster4_3_sym_copy.pdb #1/A)
> select add #1
14308 atoms, 14707 bonds, 52 pseudobonds, 1781 residues, 5 models selected
> select subtract #1
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> hide #!1 models
> show #!3 models
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 403 residues changed
> show #!2 models
> ui tool show "Renumber Residues"
> renumber #3/B:1067-1466 seqStart 67
400 residues renumbered
> select #2:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3:67
Nothing selected
> renumber #3/B:467-866 start 67
400 residues renumbered
> select #3:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!4 models
> select #4:1-1000
4362 atoms, 4483 bonds, 15 pseudobonds, 543 residues, 3 models selected
> select #4/A:1-1000
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #4/B:1-1000
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select ~sel
60638 atoms, 62326 bonds, 230 pseudobonds, 7556 residues, 20 models selected
> show #!2 models
> hide #!4 models
> show #!4 models
> select add #4
61730 atoms, 63448 bonds, 237 pseudobonds, 7696 residues, 20 models selected
> select clear
> select #4/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> hide #!2 models
> select
61730 atoms, 63448 bonds, 237 pseudobonds, 7696 residues, 20 models selected
> select clear
> select #4/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #4/B,C,D
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> select #4/B:1000-7000
3406 atoms, 3500 bonds, 19 pseudobonds, 432 residues, 3 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> show #!5 models
> hide #!4 models
> select #5/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select #4/B:0-999,2000-7000
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> select #5/B:0-999,2000-7000
3341 atoms, 3433 bonds, 19 pseudobonds, 426 residues, 3 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> show #!4 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> select #5/A
Nothing selected
> select #6/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #6/B:0-1999,3000-7000
3448 atoms, 3544 bonds, 25 pseudobonds, 433 residues, 3 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> select #7/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/B:0-2999
3299 atoms, 3389 bonds, 13 pseudobonds, 425 residues, 3 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
Drag select of 42 atoms, 44 bonds, 6 pseudobonds
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> show #!6 models
> show #!5 models
> show #!4 models
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> changechains sel A
Chain IDs of 140 residues changed
> select #4/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #6
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> changechains sel C
Chain IDs of 139 residues changed
> changechains sel C
Chain IDs of 0 residues changed
> select add #7
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #6
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> select add #6
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #6
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> changechains sel D
Chain IDs of 146 residues changed
> select subtract #7
Nothing selected
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> select add #6
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> renumber #6/C start 2
139 residues renumbered
> show #!5 models
> select subtract #6
Nothing selected
> hide #!6 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> select add #7
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> renumber #7/D:3002-3146 start 2
145 residues renumbered
> show #!6 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select subtract #7
Nothing selected
> show #!2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select ::name="HEM"
462 atoms, 484 bonds, 66 pseudobonds, 11 residues, 12 models selected
> select ::name="H4B"::name="HAR"::name="HEM"
582 atoms, 596 bonds, 74 pseudobonds, 19 residues, 12 models selected
> select ::name="HAR"
52 atoms, 40 bonds, 8 pseudobonds, 4 residues, 6 models selected
> select clear
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> changechains sel AH
Chain IDs of 140 residues changed
> select add #5
2249 atoms, 2311 bonds, 12 pseudobonds, 286 residues, 4 models selected
> select subtract #4
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> changechains sel BH
Chain IDs of 146 residues changed
> changechains sel BH
Chain IDs of 0 residues changed
> select add #6
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #5
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> changechains sel CH
Chain IDs of 139 residues changed
> select add #7
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #6
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> changechains sel DH
Chain IDs of 146 residues changed
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> select clear
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #4/AH:201@NB
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #4/AH:201@NB N 3 geometry trigonal resName UNL
> select #4/AH:201@HB1
1 atom, 1 residue, 1 model selected
> help help:credits.html
> hide sel atoms
> delete atoms sel
> delete bonds sel
> select #4/AH:201@HB2
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
You must select exactly one atom to modify.
[Repeated 1 time(s)]Drag select of 1 residues
> select #4/AH:201@NB
1 atom, 1 residue, 1 model selected
> build modify #4/AH:201@NB N 2 geometry trigonal
[Repeated 1 time(s)]
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> select clear
No visible atoms or bonds selected
> select add #4.1
6 pseudobonds, 1 model selected
> select subtract #4.2
6 pseudobonds, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4.1
6 pseudobonds, 1 model selected
> close #4.1
> hide #4.2 models
> show #!5 models
> hide #!4 models
> select add #5.1
6 pseudobonds, 1 model selected
> select subtract #5.2
6 pseudobonds, 1 model selected
> select subtract #5.1
Nothing selected
> select add #5.1
6 pseudobonds, 1 model selected
> select subtract #5.2
6 pseudobonds, 1 model selected
> close #5.1
> select #5/BH:1201@NB
1 atom, 1 residue, 1 model selected
> show sel cartoons
> ui tool show "Build Structure"
> build modify #5/BH:1201@NB N 2 geometry trigonal resName UNL
> build modify #5/BH:1201@NB N 2 geometry trigonal
> style sel stick
Changed 1 atom style
> select clear
> show #!6 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> select add #7.1
6 pseudobonds, 1 model selected
> select subtract #7.2
6 pseudobonds, 1 model selected
> close #7.1
> select #7/DH:3148@NB
1 atom, 1 residue, 1 model selected
> build modify #7/DH:3148@NB N 2 geometry trigonal
> select #7/DH:3148@HB1
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> undo
[Repeated 2 time(s)]
> select #7/DH:3148@HB1
1 atom, 1 residue, 1 model selected
> select #7/DH:3148@HB1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/DH:3148@NB
1 atom, 1 residue, 1 model selected
> build modify #7/DH:3148@NB N 2 geometry trigonal
> style sel stick
Changed 1 atom style
> select clear
> show #!6 models
> hide #!7 models
> show #!5 models
> hide #!6 models
> select #5/BH:1201@C4A
1 atom, 1 residue, 1 model selected
> select #5/BH:1201@C4A
1 atom, 1 residue, 1 model selected
> select #5/BH:1201@C4A
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 46 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #5/BH:1201@ND
1 atom, 1 residue, 1 model selected
> build modify #5/BH:1201@ND N 3 geometry tetrahedral
> build modify #5/BH:1201@ND N 2 geometry tetrahedral
> build modify #5/BH:1201@ND N 2 geometry tetrahedral resName HEM
> show #!4 models
> hide #!5 models
> select #4/AH:201@NB
1 atom, 1 residue, 1 model selected
> build modify #4/AH:201@NB N 2 geometry tetrahedral resName HEM
> show #!5 models
> show #!7 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> combine #1
> hide #!1 models
> hide #!8 models
> show #!8 models
> select #7 \- #7:3147
Expected a keyword
> select #7! #7:3147
Expected an objects specifier or a keyword
> select #7!~#7:3147
Expected an objects specifier or a keyword
> select #7~#7:3147
Expected an objects specifier or a keyword
> select #7 &~ #7:3147
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> select #8 &~ #8:3147
10996 atoms, 11301 bonds, 38 pseudobonds, 1377 residues, 3 models selected
> hide #!8 models
> show #!8 models
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> hide #!8 models
> show #!8 models
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> hide #!8 models
> show #!8 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> combine #6,8 close true modelId 6 name HB_C
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6/Z:3147@NB
1 atom, 1 residue, 1 model selected
> build modify #6/Z:3147@NB N 2 geometry tetrahedral colorByElement false
> undo
> select #6/Z:3147@HB1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #6.1
6 pseudobonds, 1 model selected
> close #6.1
> select #6/Z:3147@NB
1 atom, 1 residue, 1 model selected
> build modify #6/Z:3147@NB N 2 geometry trigonal colorByElement false
> style sel stick
Changed 1 atom style
> color sel byelement
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!7 models
> combine #2-7 name culster4_3_renumber
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> build modify #8/B:1010@NB N 2 geometry trigonal colorByElement false
> select #8/B:1010@HB2
1 atom, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #8/B:1010@HB2
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@HB1
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
You must select exactly one atom to modify.
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> build modify #8/B:1010@NB N 2 geometry trigonal colorByElement false
> hide #8.1 models
> show #8.1 models
> select #8/B:1010@HB2
1 atom, 1 residue, 1 model selected
> select #8/B:1010@HB1
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@HB2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> select clear
> select #8/B:1010@C1B
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@NB
2 atoms, 1 residue, 1 model selected
> bond sel
Created 1 bond
> select clear
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@C4B
2 atoms, 1 residue, 1 model selected
> bond sel
Created 1 bond
> color sel byelement
> select #8/B:1010@C4B
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #8/B:1010@C4B
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select #8/A:510@NB
1 atom, 1 residue, 1 model selected
> build modify #8/A:510@NB N 2 geometry trigonal colorByElement false
> select #8/A:510@HB1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #8/A:510@C4B
1 atom, 1 residue, 1 model selected
> select #8/A:510@NB
1 atom, 1 residue, 1 model selected
> select add #8/A:510@C4B
2 atoms, 1 residue, 1 model selected
> bond sel
Created 1 bond
> select clear
> select #8/A:510@NB
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> color sel byelement
> select #8/B:422
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #8/B:424
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> hide #!8 models
> show #!8 models
> combine #8 name cluster4_3_renumber_copy
> ui tool show Matchmaker
> matchmaker #9/B to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> hide #!8 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #9/B to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> select #8/A
3270 atoms, 3363 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #9/B
3270 atoms, 3364 bonds, 8 pseudobonds, 403 residues, 2 models selected
> matchmaker #9/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain A (#9), sequence alignment score = 3624.4
RMSD between 400 pruned atom pairs is 0.000 angstroms; (across all 400 pairs:
0.000)
> matchmaker #9/B to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> hide #!8 models
> show #!1 models
> select clear
> select #1:1-999
4362 atoms, 4483 bonds, 15 pseudobonds, 543 residues, 3 models selected
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> hide #!9 models
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> matchmaker #1/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with
cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1), sequence alignment score
= 3624.4
RMSD between 400 pruned atom pairs is 0.000 angstroms; (across all 400 pairs:
0.000)
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!9 models
> matchmaker #1/A & sel to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with
cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1), sequence alignment score
= 2078.6
RMSD between 400 pruned atom pairs is 0.240 angstroms; (across all 400 pairs:
0.240)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!9 models
> select #9/B:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 12 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> matchmaker #9/B & sel to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> select #9/A:219
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
2874 atoms, 2957 bonds, 359 residues, 1 model selected
> matchmaker #9/A & sel to #8/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain B (#8) with cluster4_3_renumber_copy,
chain A (#9), sequence alignment score = 1866.5
RMSD between 359 pruned atom pairs is 0.167 angstroms; (across all 359 pairs:
0.167)
> show #!8 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
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.cxs
——— End of log from Tue Jan 24 12:31:18 2023 ———
opened ChimeraX session
> select /AH
3276 atoms, 3372 bonds, 420 residues, 3 models selected
> ui tool show "Color Actions"
> show sel & #!8-9 surfaces
> color sel green target s
> color sel medium sea green target s
> color sel medium spring green target s
> color sel dark turquoise target s
> color sel medium aquamarine target s
> color sel light green target s
> color sel sea green target s
> color sel medium sea green target s
> select /CH
3150 atoms, 3234 bonds, 417 residues, 3 models selected
> show sel & #!8-9 surfaces
> color sel pale green target s
> color sel light green target s
> color sel medium sea green target s
> select /AH
3276 atoms, 3372 bonds, 420 residues, 3 models selected
> color sel pale green target s
> color sel light green target s
> select /BH
3471 atoms, 3573 bonds, 438 residues, 3 models selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color sel medium turquoise target s
> show sel & #!8-9 surfaces
> select /BH
3471 atoms, 3573 bonds, 438 residues, 3 models selected
> show sel & #!8-9 surfaces
> color sel medium turquoise target s
> color sel light sea green target s
> color sel steel blue target s
> color sel light sea green target s
> color sel medium turquoise target s
> color sel turquoise target s
> color sel medium turquoise target s
> color sel light sea green target s
> hide sel & #!8-9 surfaces
> hide #!9 models
> hide #!8 models
> select add #8
13352 atoms, 13739 bonds, 17 pseudobonds, 1670 residues, 7 models selected
> select add #9
23233 atoms, 23905 bonds, 34 pseudobonds, 2902 residues, 11 models selected
> select subtract #8
12195 atoms, 12548 bonds, 17 pseudobonds, 1524 residues, 10 models selected
> select subtract #9
1157 atoms, 1191 bonds, 146 residues, 4 models selected
> select subtract #5
Nothing selected
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> hide sel surfaces
> select clear
> hide #!8 models
> show #!9 models
> select add #9
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> hide sel surfaces
> select clear
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> ui tool show Matchmaker
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!1 models
> matchmaker #!9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1) with
cluster4_3_renumber_copy, chain A (#9), sequence alignment score = 3624.4
RMSD between 400 pruned atom pairs is 0.000 angstroms; (across all 400 pairs:
0.000)
> select add #1
11038 atoms, 11345 bonds, 44 pseudobonds, 1378 residues, 3 models selected
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> 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 #!1 models
> show #!8 models
> hide #!9 models
> show #!1 models
> hide #!8 models
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!1 models
> select #8/B:165
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
115 atoms, 117 bonds, 14 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> matchmaker #!8 & sel to #1 & sel
No 'to' model specified
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> select subtract #8
3 models selected
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #8/B
3270 atoms, 3364 bonds, 8 pseudobonds, 403 residues, 2 models selected
> show #!1 models
> hide #!8 models
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> show #!8 models
> select #8/A
3270 atoms, 3363 bonds, 9 pseudobonds, 403 residues, 3 models selected
> matchmaker #!8 & sel to #1 & sel
No 'to' model specified
> help help:user
> hide #!1 models
> hide #!8 models
> show #!1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> matchstruct #8/A to #1:1000-1999
Unknown command: matchstruct #8/A to #1:1000-1999
> matchmaker #8/A to #1:1000-1999
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1) with
culster4_3_renumber, chain A (#8), sequence alignment score = 2078.6
RMSD between 400 pruned atom pairs is 0.240 angstroms; (across all 400 pairs:
0.240)
> show #!9 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!9 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
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> select subtract #8
3 models selected
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.cxs
> color dark goldenrod target s
> select /AH
3276 atoms, 3372 bonds, 420 residues, 3 models selected
> select clear
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> show sel surfaces
> select clear
> select add #9
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> show sel surfaces
> select subtract #9
6 models selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 surfaces
> close #9.3-8
> close #9.2
> select #9/AH,BH,CH,DH
4456 atoms, 4584 bonds, 571 residues, 1 model selected
> show sel surfaces
> show #!8 models
> select clear
> help help:user
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.glb
> save /Users/cruzp2/cluster4_3_renumber_2Hb_texture.glb models #8-9
> textureColors true
> open 5f8m
Summary of feedback from opening 5f8m fetched from pdb
---
notes | Fetching compressed mmCIF 5f8m from
http://files.rcsb.org/download/5f8m.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD POP from http://ligand-expo.rcsb.org/reports/P/POP/POP.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
5f8m title:
Enterovirus 71 Polymerase Elongation Complex (C3S4/5 Form) [more info...]
Chain information for 5f8m #10
---
Chain | Description | UniProt
A | Genome polyprotein | E5RPG2_9ENTO
B | RNA (35-MER) |
C | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*CP*U)-3') |
Non-standard residues in 5f8m #10
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
POP — pyrophosphate 2-
SO4 — sulfate ion
ZN — zinc ion
> show #!10 target m
> hide #!8 models
> hide #!9 models
> close #10
> show #!8 models
> show #!9 models
> open 4r8i
Summary of feedback from opening 4r8i fetched from pdb
---
notes | Fetching compressed mmCIF 4r8i from
http://files.rcsb.org/download/4r8i.cif
Fetching CCD 0G from http://ligand-expo.rcsb.org/reports/0/0G/0G.cif
Fetching CCD 0C from http://ligand-expo.rcsb.org/reports/0/0C/0C.cif
Fetching CCD 0A from http://ligand-expo.rcsb.org/reports/0/0A/0A.cif
Fetching CCD 0U from http://ligand-expo.rcsb.org/reports/0/0U/0U.cif
Fetching CCD 0U1 from http://ligand-expo.rcsb.org/reports/0/0U1/0U1.cif
Fetching CCD SR from http://ligand-expo.rcsb.org/reports/S/SR/SR.cif
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif
4r8i title:
High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in
Complex with the Chemokine CCL2 [more info...]
Chain information for 4r8i #10
---
Chain | Description | UniProt
A | C-C motif chemokine 2 | CCL2_HUMAN
B | Mirror-Image RNA Oligonucleotide Aptamer NOXE36 |
Non-standard residues in 4r8i #10
---
0A — L-adenosine-5'-monophosphate
0U1 — 2'-methylselenyl-2'-deoxy-L-uridine-5'-monophosphate
K — potassium ion
NA — sodium ion
SR — strontium ion
> hide #!8 models
> hide #!9 models
> close #10
> show #!9 models
> show #!8 models
> show #!2 models
> select add #2
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> hide #!2 models
> save /Users/cruzp2/Desktop/enos_2Hb.cxs
——— End of log from Thu Jan 26 11:18:44 2023 ———
opened ChimeraX session
> select subtract #2
Nothing selected
> hide #9.2 models
> hide #9.3 models
> hide #9.4 models
> hide #9.5 models
> hide #8.8 models
> hide #8.7 models
> hide #8.6 models
> hide #8.5 models
> hide #8.4 models
> hide #8.3 models
> hide #8.2 models
> hide #9.1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> select #9/A,B
6540 atoms, 6727 bonds, 16 pseudobonds, 806 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!8 models
> select #8/A:210
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/A
3270 atoms, 3363 bonds, 9 pseudobonds, 403 residues, 3 models selected
> ui tool show "Color Actions"
> color sel goldenrod
> color sel sandy brown
> color sel goldenrod
[Repeated 1 time(s)]
> color sel dark orange
> color sel goldenrod
> color sel dark goldenrod
> color sel dark khaki
> color sel khaki
> ui tool show "Color Actions"
> color sel goldenrod
> show sel surfaces
> select #8/B
3270 atoms, 3364 bonds, 8 pseudobonds, 403 residues, 2 models selected
> color sel sandy brown
[Repeated 1 time(s)]
> show sel surfaces
> select #8/AH
1092 atoms, 1124 bonds, 140 residues, 1 model selected
> help help:user
> color sel dark turquoise
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel medium aquamarine
> color sel teal
> color sel medium aquamarine
> color sel cadet blue
> color sel aquamarine
> color sel dark green
> color sel aquamarine
> color sel pale green
> color sel dark sea green
> color sel pale green
> show sel surfaces
> lighting full
> select #8/AH
1092 atoms, 1124 bonds, 140 residues, 1 model selected
> color sel pale green
> color sel light green
> color sel dark sea green
> color sel pale green
> color sel medium aquamarine
> color sel green yellow
> color sel lime
> color sel chartreuse
> color sel lawn green
> color sel spring green
> color sel sea green
> color sel medium sea green
> color sel light sea green
[Repeated 1 time(s)]
> color sel medium aquamarine
> color sel light green
> color sel pale green
> color sel light green
> color sel aquamarine
> color sel light sea green
> color sel light green
> lighting soft
> lighting full
> lighting simple
> color sel light green
> color sel dark khaki
> color sel dark turquoise
> color sel medium spring green
> color sel light green
> color sel pale green
> color sel light green
> hide #!9 models
> select #8/CH
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sea green
> color sel medium sea green
> color sel light green
> color sel dark sea green
> show sel surfaces
> color sel dark sea green
> select #8/CB
Nothing selected
> select #8/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel medium aquamarine
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel pale turquoise
> color sel teal
> color sel steel blue
> show sel surfaces
> color sel blue
> color sel royal blue
> color sel dodger blue
> color sel light sky blue
> color sel sky blue
> color sel light blue
> color sel sky blue
> color sel turquoise
> color sel medium turquoise
> lighting simple
> lighting soft
> lighting full
> color sel dark turquoise
> color sel cyan
> color sel medium aquamarine
> color sel dark turquoise
> color sel turquoise
> hide #8.6 models
> show #8.6 models
> hide #8.4 models
> hide #!8 models
> show #!9 models
> show #9.2 models
> show #9.4 models
> hide #!9 models
> open 6bb5
6bb5 title:
Human Oxy-Hemoglobin [more info...]
Chain information for 6bb5 #10
---
Chain | Description | UniProt
A | Hemoglobin subunit alpha | HBA_HUMAN
B | Hemoglobin subunit beta | HBB_HUMAN
Non-standard residues in 6bb5 #10
---
HEM — protoporphyrin IX containing Fe (HEME)
OXY — oxygen molecule
6bb5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> select #10/B:132
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
283 atoms, 285 bonds, 20 residues, 1 model selected
> select up
2210 atoms, 2239 bonds, 145 residues, 1 model selected
> open rcsb_bio:6bb5
Summary of feedback from opening 6bb5 fetched from rcsb_bio
---
note | Fetching compressed 6bb5 bioassembly 1 from
https://files.rcsb.org/download/6bb5-assembly1.cif
6bb5 bioassembly 1 title:
Human Oxy-Hemoglobin [more info...]
Chain information for 6bb5 bioassembly 1 #11
---
Chain | Description
A A-2 | Hemoglobin subunit alpha
B B-2 | Hemoglobin subunit beta
Non-standard residues in 6bb5 bioassembly 1 #11
---
HEM — protoporphyrin IX containing Fe (HEME)
OXY — oxygen molecule
Opened 1 biological assemblies for 6bb5
> close #10
> select #11/A:4
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
208 atoms, 210 bonds, 14 residues, 1 model selected
> select up
2098 atoms, 2126 bonds, 139 residues, 1 model selected
> color sel aquamarine
> select #11//chain_id='A-2':77
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
67 atoms, 67 bonds, 5 residues, 1 model selected
> select up
2098 atoms, 2126 bonds, 139 residues, 1 model selected
> color sel dark sea green
> select #11/B:53
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
90 atoms, 90 bonds, 7 residues, 1 model selected
> select up
2210 atoms, 2239 bonds, 145 residues, 1 model selected
> color sel orchid
> select clear
> select add #11
9134 atoms, 9038 bonds, 16 pseudobonds, 794 residues, 2 models selected
> show sel surfaces
> hide #11.2 models
> show #11.2 models
> hide #11.3 models
> show #11.3 models
> hide #!11 models
> show #!11 models
> hide #11.1 models
> show #11.1 models
> hide #11.2 models
> show #11.2 models
> hide #11.3 models
> show #11.3 models
> close #11
> show #!8 models
> select #8/CH:78
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
192 atoms, 194 bonds, 27 residues, 2 models selected
> select up
1050 atoms, 1078 bonds, 139 residues, 2 models selected
> show sel surfaces
> select #8/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel dark turquoise
> color sel cyan
> color sel turquoise
[Repeated 2 time(s)]
> select #8/DH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel dark turquoise
[Repeated 1 time(s)]
> show sel surfaces
> color sel deep sky blue
> color sel dark turquoise
> color sel medium turquoise
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel steel blue
[Repeated 2 time(s)]
> color sel slate gray
> color sel royal blue
> color sel aquamarine
> color sel sky blue
[Repeated 1 time(s)]
> color sel light sky blue
[Repeated 1 time(s)]
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> color sel powder blue
> color sel light sky blue
> color sel light blue
> color sel light sky blue
> select #8/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel turquoise
[Repeated 2 time(s)]
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
> select ::name="HEM"
1008 atoms, 1088 bonds, 72 pseudobonds, 24 residues, 14 models selected
> color sel byelement
> select ::name="HAR"
104 atoms, 80 bonds, 16 pseudobonds, 8 residues, 10 models selected
> color sel byelement
> select ::name="H4B"
136 atoms, 144 bonds, 8 residues, 5 models selected
> color sel byelement
[Repeated 1 time(s)]
> show #!9 models
> select #9/AH
1092 atoms, 1124 bonds, 140 residues, 1 model selected
> color sel light green
> select #9/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel sky blue
> color sel light blue
> show sel surfaces
> select #9/CH
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> color sel dark olive green
> color sel dark slate gray
> color sel dark sea green
> select #9/DH:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/DH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel light sky blue
> show sel surfaces
> select ::name="HEM"
1008 atoms, 1088 bonds, 72 pseudobonds, 24 residues, 14 models selected
> color sel byelement
> select clear
> select add #9
11038 atoms, 11357 bonds, 16 pseudobonds, 1378 residues, 2 models selected
> help help:user
> transparency sel 50 target s
> transparency sel 50 target r
> transparency sel 30 target r
> transparency sel 20 target r
> transparency sel 0 target r
> transparency sel 30 target s
> hide #!9 models
> show #!9 models
> select clear
> select #9/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel light blue
[Repeated 1 time(s)]
> color sel turquoise
> color sel light blue
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
> select #9/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> transparency sel 30 target s
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
> hide #!9 models
> hide #8.5 models
> select #8/BH:4-17
Nothing selected
> hide #8.3 models
> hide #8.4 models
> hide #8.6 models
> hide #8.7 models
> hide #8.8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/B #8/A #8/B #9/A #9/B
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #8/DH
Alignment identifier is 8/DH
> sequence chain #8/BH
Alignment identifier is 8/BH
> ui tool show "Renumber Residues"
> renumber #8/BH:1002-1146 seqStart 2
145 residues renumbered
> ui tool show "Renumber Residues"
> renumber #8/BH:141-285 start 2
145 residues renumbered
> select #8/BH:4-17
106 atoms, 108 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel red
> select #8/BH:117-126
82 atoms, 86 bonds, 10 residues, 1 model selected
> color sel green
> select #8/BH:87-97
89 atoms, 90 bonds, 11 residues, 1 model selected
> select #8/DH:87-97
89 atoms, 90 bonds, 11 residues, 1 model selected
> color sel blue
> select #8/A:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:108
Nothing selected
> select #8/A:106
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
——— End of log from Tue Jan 31 14:24:37 2023 ———
opened ChimeraX session
> select #8/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/B:480
Nothing selected
> select #8/B:460
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:108-466
2874 atoms, 2957 bonds, 359 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber #8/B:108-466 start 122
359 residues renumbered
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> select #8/B:117-126
40 atoms, 39 bonds, 5 residues, 1 model selected
> select #8/BH:117-126
82 atoms, 86 bonds, 10 residues, 1 model selected
> color sel lime
> color sel spring green
> color sel chartreuse
> color sel medium spring green
> color sel yellow green
> color sel chartreuse
> color sel lime green
> color sel sea green
> color sel green
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> show #!5 models
> hide #!5 models
> show #8.5 models
> show #8.8 models
> show #8.7 models
> show #8.6 models
> show #!9 models
> hide #!9 models
> show #8.4 models
> show #8.3 models
> hide #8.8 models
> hide #8.7 models
> hide #8.6 models
> hide #8.5 models
> hide #8.4 models
> hide #8.3 models
> select #8/BH:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color sel byelement
> select #8/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel byelement
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #8/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> select #8/B:97@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> color sel byelement
> select #8/B:98
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> select #8/BH:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #8/BH:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> select #8/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:96
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> select #8/B:98
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #8/AH
Alignment identifier is 8/AH
> select #8/AH:9-123
870 atoms, 895 bonds, 115 residues, 1 model selected
> select #8/AH:9-135
958 atoms, 984 bonds, 127 residues, 1 model selected
> select clear
> select #8/AH:33
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/AH:33-37
43 atoms, 45 bonds, 5 residues, 1 model selected
> select #8/AH:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/AH:34-46
113 atoms, 119 bonds, 13 residues, 1 model selected
> select #8/AH:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/AH:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
> color sel purple
> select clear
> show #8.7 models
> select #8/AH:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/AH:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
> name frozen HBAX1 sel
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> open 1hbb
Summary of feedback from opening 1hbb fetched from pdb
---
note | Fetching compressed mmCIF 1hbb from
http://files.rcsb.org/download/1hbb.cif
1hbb title:
High-resolution X-ray study of deoxyhemoglobin rothschild 37Β TRP-> arg: A
mutation that creates an intersubunit chloride-binding site [more info...]
Chain information for 1hbb #10
---
Chain | Description | UniProt
A C | HEMOGLOBIN A (DEOXY) (ALPHA CHAIN) | HBA_HUMAN
B D | HEMOGLOBIN A (DEOXY) (BETA CHAIN) | HBB_HUMAN
Non-standard residues in 1hbb #10
---
HEM — protoporphyrin IX containing Fe (HEME)
> hide #!8 models
> select #10/A
1176 atoms, 1143 bonds, 5 pseudobonds, 206 residues, 2 models selected
> show #!8 models
> hide #!10 models
> hide #8.7 models
> select #10/A:34-42
74 atoms, 76 bonds, 9 residues, 1 model selected
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!8 models
> show #!9 models
> select #8/A:34-43
Nothing selected
> select #8/AH:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
> color (#!8 & sel) yellow
> color (#!8 & sel) orange
> color (#!8 & sel) cyan
> color (#!8 & sel) dark gray
> color (#!8 & sel) gray
> color (#!8 & sel) yellow
> select clear
> show #8.3 models
> help help:user
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> hide #9
> undo
> hide #9 target m
> show #9 target m
> alias list
> show #8.4 models
> show #8.5 models
> show #8.6 models
> show #8.7 models
> show #8.8 models
> close #10
> ui tool show AlphaFold
> alphafold match #8/A
Fetching compressed AlphaFold A0A2R9BVK1 from
https://alphafold.ebi.ac.uk/files/AF-A0A2R9BVK1-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A2R9BVK1 (chain
A)
AlphaFold chains matching culster4_3_renumber
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | A0A2R9BVK1_PANPA | A0A2R9BVK1 | 0.57 | 562 | 400 | 78
Opened 1 AlphaFold model
> close #10
> alphafold match NOS3_HUMAN
1 AlphaFold model found using UniProt identifier: P29474 (UniProt NOS3_HUMAN)
Opened 1 AlphaFold model
> ui tool show Matchmaker
> matchmaker #10/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with AlphaFold NOS3_HUMAN, chain
A (#10), sequence alignment score = 1966.4
RMSD between 392 pruned atom pairs is 0.618 angstroms; (across all 400 pairs:
1.170)
> hide #8.6 models
Fetching PAE using AlphaFold database version 2
> alphafold pae #10 uniprotId P29474 version 2
Fetching compressed AlphaFold PAE P29474 from
https://alphafold.ebi.ac.uk/files/AF-P29474-F1-predicted_aligned_error_v2.json
> color #10:64-475 lime
> color #10:1155-1203 lime
> color #10:1-69 lime
> color #10:519-721 lime
> alphafold pae #10 colorDomains true
> show #8.6 models
> alphafold match NOS3_HUMAN
1 AlphaFold model found using UniProt identifier: P29474 (UniProt NOS3_HUMAN)
Opened 1 AlphaFold model
> matchmaker #11/A to #8/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain B (#8) with AlphaFold NOS3_HUMAN, chain
A (#11), sequence alignment score = 1995.4
RMSD between 389 pruned atom pairs is 0.624 angstroms; (across all 400 pairs:
1.170)
> alphafold pae #10 colorDomains true
Fetching PAE using AlphaFold database version 2
> alphafold pae #11 uniprotId P29474 version 2
> alphafold pae #11 colorDomains true
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session_AF.cxs
> help help:user
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/rosetta_reductase/VR/r_0409_3.pdb
Summary of feedback from opening /Users/cruzp2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/eNOS_Hba/rosetta_reductase/VR/r_0409_3.pdb
---
warnings | Ignored bad PDB record found on line 9209
CAPRI_rank 0
Ignored bad PDB record found on line 9210
Fnat 0
Ignored bad PDB record found on line 9211
I_sc -24.5951
Ignored bad PDB record found on line 9212
Irms 14.1115
Ignored bad PDB record found on line 9213
Irms_leg 13.0251
590 messages similar to the above omitted
Chain information for r_0409_3.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> open 1umk
1umk title:
The Structure of Human Erythrocyte NADH-cytochrome b5 Reductase [more info...]
Chain information for 1umk #13
---
Chain | Description | UniProt
A | NADH-cytochrome b5 reductase | NCB5R_HUMAN
Non-standard residues in 1umk #13
---
FAD — flavin-adenine dinucleotide
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #13 to #12/C pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 r_0409_3.pdb, chain C (#12) with 1umk, chain A (#13), sequence
alignment score = 1431.6
RMSD between 271 pruned atom pairs is 0.001 angstroms; (across all 271 pairs:
0.001)
> combine #12,13 name r_0409_3_FAD
Remapping chain ID 'A' in 1umk #13 to 'D'
> hide #!9 models
> hide #10 models
> ui tool show Matchmaker
> matchmaker #!14 to #8/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 culster4_3_renumber, chain A (#8) with r_0409_3_FAD, chain A (#14),
sequence alignment score = 618.2
RMSD between 104 pruned atom pairs is 0.042 angstroms; (across all 180 pairs:
21.551)
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #11 models
> show #11 models
> show #10 models
> hide #!12 models
> hide #13 models
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel byelement
> style sel & #!14 sphere
Changed 53 atom styles
> select clear
> select add #14
12167 atoms, 11579 bonds, 33 pseudobonds, 1602 residues, 2 models selected
> show sel surfaces
> hide #14.5 models
> show #14.5 models
> hide #14.5 models
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 2 models selected
> hide #!14 models
> show #!14 models
> hide #14.2 models
> hide #14.3 models
> hide #14.4 models
> show #14.5 models
> hide #14.5 models
> show #14.5 models
> hide #14.5 models
> select #14/A,B,C
9196 atoms, 9296 bonds, 33 pseudobonds, 577 residues, 2 models selected
> hide sel cartoons
> select #14/A,B,C
9196 atoms, 9296 bonds, 33 pseudobonds, 577 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> show #14.5 models
> hide #14.5 models
> show #14.5 models
> hide #14.5 models
> select #14/D
2971 atoms, 2283 bonds, 1025 residues, 1 model selected
> show sel surfaces
> color #14 #12894cff
> hide #14.5 models
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 2 models selected
> color sel byelement target cspf
[Repeated 1 time(s)]
> color sel byelement
> select clear
> show #14.5 models
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk.cxs
——— End of log from Wed Feb 1 14:51:18 2023 ———
opened ChimeraX session
> select ::name="FAD"::name="H4B"::name="HAR"::name="HEM"::name="HOH"
2860 atoms, 1428 bonds, 88 pseudobonds, 1548 residues, 16 models selected
> style sel & #!8,14 sphere
Changed 1118 atom styles
> select clear
[Repeated 1 time(s)]
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #1-7
> help help:user
> combine #8 close true model(D 1 name cluster4_4_renumber
Expected a keyword
> combine #8 close true modelID 1 name cluster4_4_renumber
Expected a keyword
> combine #8 close true modelID #1 name cluster4_4_renumber
Expected a keyword
> combine #8 close true modelID #1
Expected a keyword
> combine #8 close true modelID 1
Expected a keyword
> combine #8 modelID 1
Expected a keyword
> combine #8
> close #1
> combine #8.1-8
No structures specified
> combine #8,8.1-8
No structures specified
> rename #8 cluster_4_3_renumber id 1
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #10 models
> hide #11 models
> show #11 models
> show #10 models
> show #!1 models
> rename #2 cluster_4_3_renumber_copy id 2
> rename #9 cluster_4_3_renumber_copy id 2
> show #!2 models
> rename #14 rosetta_0409_3_FAD id 3
> rename #10 AlphaFold NOS3_HUMAN id 4
Expected a keyword
> rename #10 AlphaFold_NOS3_HUMAN id 4
> rename #11 AlphaFold_NOS3_HUMAN_copy id 5
> close #13#12
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
> hide #5 models
> hide #4 models
> hide #!3 models
> hide #!2 models
> hide #1.8 models
> hide #1.7 models
> hide #1.6 models
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> select #1/BH,CH,DH
3364 atoms, 3460 bonds, 431 residues, 1 model selected
> select #1/BH,CH,DH,Z
3406 atoms, 3506 bonds, 432 residues, 1 model selected
> select #1/AH,BH,CH,DH,Z
4498 atoms, 4630 bonds, 572 residues, 1 model selected
> name HB1 #1/AH,BH,CH,DH,Z
> hide sel atoms
> hide sel cartoons
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
——— End of log from Thu Feb 2 10:34:00 2023 ———
opened ChimeraX session
> alias a show #1/AH target r;show #1:201;~sel
> a
Nothing selected
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_a.cxs
> alias b show #1/BH,CH,DH,Z target r;show #1:201,1201,3147,3148 target a;~sel
> b
Nothing selected
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_b.cxs
> alias c show #1/BH:6
> alias c show #1/BH:6 target
> alias c show #1/BH:6 target a
> c
> help help:user
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_c.cxs
> show #1.3
> hide #1.3
> show #1.3-1.8
> show #1.3
> hide #1.3
> show #1.3-8
> hide #1.3-8
> alias delete show #1.3-8
Expected fewer arguments
> alias delete show #1.3-8
Expected fewer arguments
> alias delete show "#1.3-8"
Expected fewer arguments
> alias e show #1.3-8
> alias dd show #1.3-8
> alias e show #1.3-8
> e
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_dd.cxs
——— End of log from Thu Feb 2 11:36:33 2023 ———
opened ChimeraX session
> meeting start andi2
Meeting "andi2" started at chimeraxmeeting.net port 52201
Participants can join with command "meeting andi2"
Connection from ::1 port 54365 established, waiting for join message
Connection accepted from ::1 port 54365
Connection from ::1 port 54369 established, waiting for join message
Connection accepted from ::1 port 54369
> lighting simple
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
[deleted a bunch of the errors to fit within ticket limits]
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1315, in _data_available
self._message_received_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1210, in _message_received
self._send_message(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1229, in _send_message
msg_stream.send_message_bytes(msg_bytes)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1459, in send_message_bytes
self._send_message_cb(msg, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 964, in _message_received
t.update_model(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1666, in update_model
PointerModels.update_model(self, msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1499, in update_model
m.update_pointer(msg)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1927, in update_pointer
for h,hm in zip(self._hand_models(len(hpos)), hpos):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in _hand_models
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/meeting/meeting.py", line 1886, in <listcomp>
new_hands = [HandModel(self.session, 'Hand %d' % (i+1), color=self._color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2857, in __init__
self._create_model_geometry(length, radius, color)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2871, in _create_model_geometry
self._buttons = b = HandButtons(self._controller_type)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/vive/vr.py", line 2916, in __init__
import openvr
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/__init__.py", line 54, in <module>
_openvr = ctypes.cdll.LoadLibrary(_openvr_lib_path)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 452, in LoadLibrary
return self._dlltype(name)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
OSError:
dlopen(/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 374, in __init__
self._handle = _dlopen(self._name, mode)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,2
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 8422.100.650
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.6.4 (21G526)
Kernel Version: Darwin 21.6.0
Time since boot: 3 days 21:49
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Thunderbolt Display:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
BenQ GW2750H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NIHPresets: 1.1.9
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (1)
comment:1 by , 3 years ago
| Component: | Unassigned → VR |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Error when additional user joins meeting |
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