![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17432 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
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"codeSigningMonitor" : 1,
"incident" : "2E998D72-0587-41C8-9E83-5C9F4C2FD157",
"pid" : 5532,
"translated" : false,
"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2025-04-18 13:47:43.9456 -0400",
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"procExitAbsTime" : 617205999979,
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"name" : "libsystem_c.dylib"
},
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"base" : 6510219264,
"size" : 31568,
"uuid" : "c35a8e3b-8974-3acf-a41f-039d834f198c",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
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"size" : 21566464,
"uuid" : "9a3b3d72-3eac-35fb-ba23-3c37820ac1d3",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.60.2"
},
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"size" : 636112,
"uuid" : "7e784dd1-c275-3489-9c7b-42983f8954ab",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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"size" : 5500928,
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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"uuid" : "fbe4abfe-8fa3-3904-8869-81f1c824eb01",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
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Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/npd1/Desktop/CasXMax paper/Figure models/K610c.cxs"
Log from Fri Dec 20 14:41:34 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/R610b.cxs format session
Log from Thu Dec 19 14:32:51 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/R610a.cxs format session
Log from Thu Dec 19 09:27:48 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/R610.cxs
Log from Thu Dec 19 08:48:26 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/R610.cxs
Log from Thu Dec 19 08:17:31 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/K610.cxs
Log from Thu Dec 19 08:04:12 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/T26a.cxs
Log from Wed Dec 18 18:16:40 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/npd1/Desktop/T26.cxs format session
Log from Wed Dec 18 17:53:52 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/npd1/Desktop/Session 3a surfaces.cxs"
Log from Tue Dec 17 16:34:16 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/npd1/Desktop/Session 2.cxs"
Log from Tue Dec 17 15:14:27 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/npd1/Desktop/CasX & CasY AF modeling/X2+X2MAX stateI & state
> II.cxs"
Log from Thu Nov 14 19:14:01 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/npd1/Downloads/X2-Max 7WAY (state I).pdb"
X2-Max 7WAY (state I).pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for X2-Max 7WAY (state I).pdb #1
---
Chain | Description
D | No description available
> open "/Users/npd1/Downloads/X2-Max 7WB0 (state III).pdb"
X2-Max 7WB0 (state III).pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for X2-Max 7WB0 (state III).pdb #2
---
Chain | Description
D | No description available
> open "/Users/npd1/Downloads/X2-Max 7WAZ (state II).pdb"
X2-Max 7WAZ (state II).pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for X2-Max 7WAZ (state II).pdb #3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-3 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 X2-Max 7WAY (state I).pdb, chain D (#1) with X2-Max 7WB0 (state
III).pdb, chain D (#2), sequence alignment score = 4510.1
RMSD between 597 pruned atom pairs is 0.734 angstroms; (across all 975 pairs:
15.887)
Matchmaker X2-Max 7WAY (state I).pdb, chain D (#1) with X2-Max 7WAZ (state
II).pdb, chain A (#3), sequence alignment score = 4935.5
RMSD between 656 pruned atom pairs is 0.994 angstroms; (across all 975 pairs:
4.408)
> select /D:26,610,808
66 atoms, 60 bonds, 6 residues, 2 models selected
> show sel atoms
> select /D:26,610,808
66 atoms, 60 bonds, 6 residues, 2 models selected
> color sel red
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #1 models
> hide #2 models
> show #2 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #3 models
> select add #3
7987 atoms, 8141 bonds, 981 residues, 3 models selected
> select add #2
15875 atoms, 16192 bonds, 1953 residues, 3 models selected
> select add #1
23763 atoms, 24243 bonds, 2925 residues, 3 models selected
> select subtract #1
15842 atoms, 16162 bonds, 1950 residues, 2 models selected
> select subtract #2
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> select /D:26,610,808
66 atoms, 60 bonds, 6 residues, 2 models selected
> select /A:26,610,808
33 atoms, 30 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel red
> show #1 models
> show #2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> open "/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2
> (cryoEM)/7way (CasX2 state I).pdb"
7way (CasX2 state I).pdb title:
Plmcasx-SGRNAV1-dsDNA ternary complex At NTS loading state [more info...]
Chain information for 7way (CasX2 state I).pdb #4
---
Chain | Description
A | dplmcasx
B | DNA (33-mer)
C | DNA (27-mer)
D | RNA
> open "/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2
> (cryoEM)/7way (CasX2 state I).pdb"
7way (CasX2 state I).pdb title:
Plmcasx-SGRNAV1-dsDNA ternary complex At NTS loading state [more info...]
Chain information for 7way (CasX2 state I).pdb #5
---
Chain | Description
A | dplmcasx
B | DNA (33-mer)
C | DNA (27-mer)
D | RNA
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2
> (cryoEM)/7waz (CasX2 state II.cif"
7waz (CasX2 state II.cif title:
PlmCasX-sgRNAv1-dsDNA ternary complex at ts loading state [more info...]
Chain information for 7waz (CasX2 state II.cif #6
---
Chain | Description | UniProt
A | dPlmCasX | A0A1G3BXR9_9BACT 1-978
B | TS-DNA |
C | NTS-DNA |
D | RNA (115-MER) |
> open "/Users/npd1/Library/CloudStorage/Dropbox/Alphafold/Structures/CasX2
> (cryoEM)/7wb0 (CasX2 state III).cif"
7wb0 (CasX2 state III).cif title:
PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state with flexible H2
domain [more info...]
Chain information for 7wb0 (CasX2 state III).cif #7
---
Chain | Description | UniProt
A | dPlmCasX | A0A1G3BXR9_9BACT 1-978
B | TS-DNA |
C | NTS-DNA |
D | RNA (115-MER) |
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #1-3#!4,6-7 to #5
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 7way (CasX2 state I).pdb, chain A (#5) with X2-Max 7WAY (state
I).pdb, chain D (#1), sequence alignment score = 5017.3
RMSD between 960 pruned atom pairs is 0.065 angstroms; (across all 960 pairs:
0.065)
Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with X2-Max 7WB0 (state
III).pdb, chain D (#2), sequence alignment score = 4468.3
RMSD between 593 pruned atom pairs is 0.731 angstroms; (across all 960 pairs:
15.989)
Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with X2-Max 7WAZ (state
II).pdb, chain A (#3), sequence alignment score = 4885.9
RMSD between 652 pruned atom pairs is 0.994 angstroms; (across all 960 pairs:
4.406)
Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with 7way (CasX2 state
I).pdb, chain A (#4), sequence alignment score = 5089.5
RMSD between 960 pruned atom pairs is 0.000 angstroms; (across all 960 pairs:
0.000)
Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with 7waz (CasX2 state
II.cif, chain A (#6), sequence alignment score = 4878.9
RMSD between 649 pruned atom pairs is 1.008 angstroms; (across all 952 pairs:
4.384)
Matchmaker 7way (CasX2 state I).pdb, chain A (#5) with 7wb0 (CasX2 state
III).cif, chain A (#7), sequence alignment score = 4690.5
RMSD between 592 pruned atom pairs is 0.737 angstroms; (across all 797 pairs:
3.068)
> hide #!5 models
> hide #!6 models
> hide #!7 models
> sequence chain #4/B
Alignment identifier is 4/B
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> nucleotides #1-3#!4 fill
> style nucleic & #1-3#!4 stick
Changed 3667 atom styles
> color #1-4 white
> undo
> select #7/B:-2-30
674 atoms, 753 bonds, 33 residues, 1 model selected
> select #7/B:-2-30
674 atoms, 753 bonds, 33 residues, 1 model selected
> select #7/B:-2-30
674 atoms, 753 bonds, 33 residues, 1 model selected
> select #7/B:-2-30
674 atoms, 753 bonds, 33 residues, 1 model selected
> nucleotides #1-3#!4 fill
> style nucleic & #1-3#!4 stick
Changed 3667 atom styles
> color #1-4 light gray
> undo
> color #4 #517a53ff
> color #4 #2851e4ff
> select add #4
12127 atoms, 12794 bonds, 3 pseudobonds, 1168 residues, 3 models selected
> select add #7
21549 atoms, 22694 bonds, 165 pseudobonds, 2107 residues, 5 models selected
> select subtract #7
11453 atoms, 12041 bonds, 3 pseudobonds, 1135 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4
11453 atoms, 12041 bonds, 3 pseudobonds, 1135 residues, 2 models selected
> color #3 #fb001dff
> color #2 #1bce0eff
> color #3 #1bce0eff
> color #1 #1bce0eff
> select clear
> select /A:26,610,808
133 atoms, 118 bonds, 15 residues, 5 models selected
> show sel & #3#!4 atoms
> color (#3#!4 & sel) red
> select /D:26,610,808
158 atoms, 160 bonds, 10 residues, 6 models selected
> color (#1-2#!4 & sel) red
> select #4/D:26
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel blue
> select #6/D:1-122
2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected
> select #6/D:1-122
2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected
> select #6/C:1-12
245 atoms, 273 bonds, 12 residues, 1 model selected
> select #6/B:1-30
614 atoms, 686 bonds, 30 residues, 1 model selected
> select #4/D:1-122
2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected
> select #4/C:1-27
547 atoms, 611 bonds, 27 residues, 1 model selected
> select #4/B:-2-30
674 atoms, 753 bonds, 33 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/C:11@O2
2 atoms, 2 residues, 2 models selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show Distances
> distance #1/D:26@NH2 #4/C:11@O2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2
state I).pdb #4/C DT 11 O2: 4.427Å
> select #4/A:610@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 1 model selected
> distance #4/A:610@NZ #4/B:22@OP1
Distance between 7way (CasX2 state I).pdb #4/A LYS 610 NZ and /B DG 22 OP1:
4.707Å
> select #4/C:25
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #4/D
2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected
> color (#!4 & sel) light gray
> color (#!4 & sel) cornflower blue
> select #3/B
Nothing selected
> select #4/B
674 atoms, 753 bonds, 33 residues, 1 model selected
> color sel light gray
> select #4/C
547 atoms, 611 bonds, 27 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> nucleotides sel fill
> style nucleic & sel stick
Changed 547 atom styles
> color sel gray
> select clear
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select #4/B:20@OP1
1 atom, 1 residue, 1 model selected
> select add #1/D:26@NH2
2 atoms, 2 residues, 2 models selected
> distance #4/B:20@OP1 #1/D:26@NH2
Distance between 7way (CasX2 state I).pdb #4/B DA 20 OP1 and X2-Max 7WAY
(state I).pdb #1/D ARG 26 NH2: 6.506Å
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:21@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/D:26@NH2 #4/B:21@OP1
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DT 21 OP1: 5.251Å
> select #4/D
2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected
> hide sel cartoons
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #3/A:26@NH2
2 atoms, 2 residues, 2 models selected
> distance #1/D:26@NH2 #3/A:26@NH2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and X2-Max 7WAZ
(state II).pdb #3/A ARG 26 NH2: 1.454Å
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:21@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #4/B:21@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DT 21 OP1: 4.148Å
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:20@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #4/B:20@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DA 20 OP1: 5.079Å
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:20@OP2
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #4/B:20@OP2
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DA 20 OP2: 5.657Å
> hide #3 models
> show #3 models
> hide #2 models
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/C:11@O2
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #4/C:11@O2
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2
state I).pdb #4/C DT 11 O2: 4.483Å
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:21@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/D:26@NH2 #4/B:21@OP2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DT 21 OP2: 5.750Å
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:21@OP2
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #4/B:21@OP2
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DT 21 OP2: 5.141Å
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:20@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/D:26@NH2 #4/B:20@OP2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2
state I).pdb #4/B DA 20 OP2: 7.074Å
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> select #3/A:610@NH1
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:610@NH1 #4/B:22@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 610 NH1 and 7way (CasX2
state I).pdb #4/B DG 22 OP1: 7.736Å
> select #1/D:610@NH1
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/D:610@NH1 #4/B:22@OP1
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH1 and 7way (CasX2
state I).pdb #4/B DG 22 OP1: 8.474Å
> select #4/A:610@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:21@OP2
2 atoms, 2 residues, 1 model selected
> distance #4/A:610@NZ #4/B:21@OP2
Distance between 7way (CasX2 state I).pdb #4/A LYS 610 NZ and /B DT 21 OP2:
4.599Å
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hbonds sel reveal true
Atom specifier selects no atoms
> hide #3 models
> hide #1 models
> select #4/B:7-10
79 atoms, 86 bonds, 4 residues, 1 model selected
> select #4/C:8-11
80 atoms, 88 bonds, 4 residues, 1 model selected
> color sel orange
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select #1/D:610@NH1
1 atom, 1 residue, 1 model selected
> select add #4/B:21@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/D:610@NH1 #4/B:21@OP2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH1 and 7way (CasX2
state I).pdb #4/B DT 21 OP2: 8.981Å
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!4 models
> show #!4 models
> hide #1 models
> show #1 models
> hide #!4 models
> show #2 models
> hide #1 models
> hide #2 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #2 models
> hide #2 models
> show #2 models
> select #2/A:26,610,808
Nothing selected
> select #2/D:26,610,808
33 atoms, 30 bonds, 3 residues, 1 model selected
> select #6/A:26,610,808
25 atoms, 22 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel lime
> color #2 #c1d228ff
> select #6/B,C,D
3305 atoms, 3693 bonds, 130 pseudobonds, 157 residues, 3 models selected
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 3305 atom styles
> hide sel cartoons
> select #6/B
614 atoms, 686 bonds, 30 residues, 1 model selected
> color sel light gray
> select #6/C
245 atoms, 273 bonds, 12 residues, 1 model selected
> color sel dim gray
> select #6/D
2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected
> color (#!6 & sel) blue
> select #2/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> select #2/D:26,610,808
33 atoms, 30 bonds, 3 residues, 1 model selected
> color sel red
> select #2/D:610@NH1
1 atom, 1 residue, 1 model selected
> select add #6/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #2/D:610@NH1 #6/B:22@OP1
Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 610 NH1 and 7waz (CasX2
state II.cif #6/B DG 22 OP1: 7.671Å
> select add #6/A:610@NZ
3 atoms, 3 residues, 2 models selected
> select #6/A:610@NZ
1 atom, 1 residue, 1 model selected
> select add #2/D:610@NH1
2 atoms, 2 residues, 2 models selected
> distance #6/A:610@NZ #2/D:610@NH1
Distance between 7waz (CasX2 state II.cif #6/A LYS 610 NZ and X2-Max 7WB0
(state III).pdb #2/D ARG 610 NH1: 4.628Å
> select subtract #6/A:610@NZ
1 atom, 1 residue, 1 model selected
> select #6/A:610@NZ
1 atom, 1 residue, 1 model selected
> select add #6/B:22@OP1
2 atoms, 2 residues, 1 model selected
> distance #6/A:610@NZ #6/B:22@OP1
Distance between 7waz (CasX2 state II.cif #6/A LYS 610 NZ and /B DG 22 OP1:
6.773Å
> select #6/A:610@NZ
1 atom, 1 residue, 1 model selected
> select add #6/B:21@OP2
2 atoms, 2 residues, 1 model selected
> distance #6/A:610@NZ #6/B:21@OP2
Distance between 7waz (CasX2 state II.cif #6/A LYS 610 NZ and /B DT 21 OP2:
4.311Å
> select add #2/D:610@NH1
3 atoms, 3 residues, 2 models selected
> select #2/D:610@NH1
1 atom, 1 residue, 1 model selected
> select add #6/B:21@OP2
2 atoms, 2 residues, 2 models selected
> distance #2/D:610@NH1 #6/B:21@OP2
Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 610 NH1 and 7waz (CasX2
state II.cif #6/B DT 21 OP2: 8.703Å
> select #2/D:26@NH2
1 atom, 1 residue, 1 model selected
> select #6/B:21@OP1
1 atom, 1 residue, 1 model selected
> select add #2/D:26@NH2
2 atoms, 2 residues, 2 models selected
> distance #6/B:21@OP1 #2/D:26@NH2
Distance between 7waz (CasX2 state II.cif #6/B DT 21 OP1 and X2-Max 7WB0
(state III).pdb #2/D ARG 26 NH2: 4.733Å
Drag select of 3 residues, 6 atoms, 5 bonds, 3 shapes
> select #6/B:20@OP1
1 atom, 1 residue, 1 model selected
> select add #2/D:26@NH2
2 atoms, 2 residues, 2 models selected
> distance #6/B:20@OP1 #2/D:26@NH2
Distance between 7waz (CasX2 state II.cif #6/B DA 20 OP1 and X2-Max 7WB0
(state III).pdb #2/D ARG 26 NH2: 4.695Å
> select #2/D:26@NH2
1 atom, 1 residue, 1 model selected
> select #2/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #6/C:12@O2
2 atoms, 2 residues, 2 models selected
> distance #2/D:26@NH2 #6/C:12@O2
Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2 and 7waz (CasX2
state II.cif #6/C DC 12 O2: 4.743Å
> select #2/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #6/B:21@OP2
2 atoms, 2 residues, 2 models selected
> distance #2/D:26@NH2 #6/B:21@OP2
Distance between X2-Max 7WB0 (state III).pdb #2/D ARG 26 NH2 and 7waz (CasX2
state II.cif #6/B DT 21 OP2: 6.180Å
> hide #!6 models
> show #1 models
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #2/D:26@NH2
2 atoms, 2 residues, 2 models selected
> distance #1/D:26@NH2 #2/D:26@NH2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and X2-Max 7WB0
(state III).pdb #2/D ARG 26 NH2: 0.743Å
> hide #1 models
> show #!6 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 #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select #6/C:9-12
79 atoms, 87 bonds, 4 residues, 1 model selected
> color sel orange
> show #!5 models
> hide #2 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!4 models
> hide #!6 models
> select #4/C:7-10
80 atoms, 88 bonds, 4 residues, 1 model selected
> color sel orange
> select #4/C:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> select #6/C:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel medium blue
> select #6/C:7-10
80 atoms, 88 bonds, 4 residues, 1 model selected
> color sel orange
> hide #!6 models
> show #1 models
> hide #1 models
> show #3 models
> hide #!4 models
> show #!6 models
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #6/B:21@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #6/B:21@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2
state II.cif #6/B DT 21 OP1: 4.033Å
> select #3/A:26@NH1
1 atom, 1 residue, 1 model selected
> select add #6/B:21@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH1 #6/B:21@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH1 and 7waz (CasX2
state II.cif #6/B DT 21 OP1: 4.895Å
> select clear
Drag select of 1 atoms
> select add #6/C:12@O2
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #6/C:12@O2
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2
state II.cif #6/C DC 12 O2: 4.603Å
> select #3/A:440
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/B:19@O3'
1 atom, 1 residue, 1 model selected
> select #6/B:20@OP1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #6/B:20@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #6/B:20@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2
state II.cif #6/B DA 20 OP1: 3.853Å
> select #6/C:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/C:12
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel medium blue
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #3 models
> show #3 models
> show #!5 models
> hide #!5 models
> hide #3 models
> hide #!4 models
> show #!4 models
> show #!6 models
> hide #!4 models
> show #3 models
> show #1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> hide #3 models
> hide #1 models
> show #!4 models
> show #!6 models
> select /C
1886 atoms, 2106 bonds, 93 residues, 4 models selected
> select #4/C:1-27
547 atoms, 611 bonds, 27 residues, 1 model selected
> select #6/B:1-30
614 atoms, 686 bonds, 30 residues, 1 model selected
> select #6/C:1-12
245 atoms, 273 bonds, 12 residues, 1 model selected
> hide #!4 models
> show #2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #3 models
> hide #1 models
> show #!6 models
> select #3/A:26@NH2
1 atom, 1 residue, 1 model selected
> select add #6/C:11@O2
2 atoms, 2 residues, 2 models selected
> distance #3/A:26@NH2 #6/C:11@O2
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 26 NH2 and 7waz (CasX2
state II.cif #6/C DT 11 O2: 8.318Å
> hide #3 models
> show #3 models
> hide #3 models
> show #1 models
> hide #!6 models
> show #!4 models
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select add #4/C:12@O2
2 atoms, 2 residues, 2 models selected
> distance #1/D:26@NH2 #4/C:12@O2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 26 NH2 and 7way (CasX2
state I).pdb #4/C DC 12 O2: 7.267Å
> hide #!4 models
> hide #1 models
> show #1 models
> show #!4 models
> hide #1 models
> show #3 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #3 models
> show #1 models
> select #4/C:21@OP2
1 atom, 1 residue, 1 model selected
> select add #1/D:808@NH1
2 atoms, 2 residues, 2 models selected
> distance #4/C:21@OP2 #1/D:808@NH1
Distance between 7way (CasX2 state I).pdb #4/C DT 21 OP2 and X2-Max 7WAY
(state I).pdb #1/D ARG 808 NH1: 0.876Å
> select #1/D:808@NH2
1 atom, 1 residue, 1 model selected
> select add #4/C:21@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/D:808@NH2 #4/C:21@OP2
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 808 NH2 and 7way (CasX2
state I).pdb #4/C DT 21 OP2: 2.158Å
> select #4/A:808@NZ
1 atom, 1 residue, 1 model selected
> select add #4/C:21@OP2
2 atoms, 2 residues, 1 model selected
> distance #4/A:808@NZ #4/C:21@OP2
Distance between 7way (CasX2 state I).pdb #4/A LYS 808 NZ and /C DT 21 OP2:
3.776Å
> show #3 models
> hide #1 models
> hide #!4 models
> show #!6 models
> select #6/A:808@NZ
1 atom, 1 residue, 1 model selected
> select add #6/B:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #6/A:808@NZ #6/B:3@OP1
Distance between 7waz (CasX2 state II.cif #6/A LYS 808 NZ and /B DT 3 OP1:
2.855Å
> select add #3/A:808@NH2
3 atoms, 3 residues, 2 models selected
> select #3/A:808@NH2
1 atom, 1 residue, 1 model selected
> select add #6/B:3@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:808@NH2 #6/B:3@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 808 NH2 and 7waz (CasX2
state II.cif #6/B DT 3 OP1: 3.209Å
> select #6/B
614 atoms, 686 bonds, 30 residues, 1 model selected
> color sel hot pink
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #6/D
Alignment identifier is 6/D
> select #4/B:-2
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/B:-2
20 atoms, 21 bonds, 1 residue, 1 model selected
Window position QRect(1985,942 575x86) outside any known screen, using primary
screen
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> select #6/D:122
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/D:110-122
282 atoms, 317 bonds, 13 residues, 1 model selected
> select #6/D:111-122
259 atoms, 291 bonds, 12 residues, 1 model selected
> select #6/D:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/D
2446 atoms, 2734 bonds, 78 pseudobonds, 115 residues, 3 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 4 time(s)]
> hide #3 models
> hide #!6 models
> show #1 models
> show #!4 models
> hide #1 models
> show #1 models
> hide #!4 models
> hide #1 models
> show #3 models
> show #!6 models
> select #3/A:808@NH1
1 atom, 1 residue, 1 model selected
> select add #6/B:3@OP1
2 atoms, 2 residues, 2 models selected
> distance #3/A:808@NH1 #6/B:3@OP1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 808 NH1 and 7waz (CasX2
state II.cif #6/B DT 3 OP1: 1.752Å
> save "/Users/npd1/Desktop/X2+X2MAX stateI & state II.cxs"
——— End of log from Thu Nov 14 19:14:01 2024 ———
opened ChimeraX session
> show #1 models
> show #2 models
> show #!4 models
> show #!5 models
> show #!7 models
> select add #1
7923 atoms, 8081 bonds, 977 residues, 3 models selected
> select add #2
15844 atoms, 16162 bonds, 1952 residues, 4 models selected
> select add #3
23764 atoms, 24243 bonds, 2926 residues, 4 models selected
> select add #4
35217 atoms, 36284 bonds, 6 pseudobonds, 4061 residues, 7 models selected
> select add #5
46670 atoms, 48325 bonds, 9 pseudobonds, 5196 residues, 9 models selected
> select add #6
57703 atoms, 59902 bonds, 145 pseudobonds, 6304 residues, 11 models selected
> select add #7
67799 atoms, 70555 bonds, 307 pseudobonds, 7276 residues, 14 models selected
> select add #8
67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected
> select subtract #8
67799 atoms, 70555 bonds, 301 pseudobonds, 7276 residues, 13 models selected
> select all
67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected
> color #1 skyblue
> select #1,2,3,4,5,6,7
67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 14 models selected
> select #1
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> select #1/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> select #2/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> hide #1 models
> hide #3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> select /D:4-978
25362 atoms, 26802 bonds, 146 pseudobonds, 2398 residues, 13 models selected
> select all
67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected
> show #1 models
> show #3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> select all
67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected
> select all
67799 atoms, 70555 bonds, 339 pseudobonds, 7276 residues, 15 models selected
> color (#1-3#!4-7 & sel) cornflower blue
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> set bgColor white
> nucleotides sel atoms
> style nucleic & sel stick
Changed 14306 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 14306 atom styles
> hide #2 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> select #1/D:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #1 models
> show #2 models
> select #2/D:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #2 models
> show #3 models
> select #3/A:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #3 models
> show #!4 models
> select #4/A:808
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #!4 models
> show #!5 models
> select #5/A:808
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel byhetero
> hide #!5 models
> show #!6 models
> select #6/A:808
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #!6 models
> show #!7 models
> select #7/A:808
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> show #!4 models
> show #!5 models
> show #!6 models
> select #4,5,6,7/B
2636 atoms, 2945 bonds, 129 residues, 4 models selected
> color sel light gray
> color sel byhetero
> nucleotides sel slab
> style nucleic & sel stick
Changed 2636 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 2636 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 2636 atom styles
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel tube/slab shape muffler
> show sel atoms
> nucleotides sel slab
> style nucleic & sel stick
Changed 2636 atom styles
> nucleotides sel tube/slab shape box
> select #4,5,6,7/C
1886 atoms, 2106 bonds, 93 residues, 4 models selected
> nucleotides sel tube/slab shape box
> color sel dark gray
> color sel dim gray
> show sel atoms
[Repeated 2 time(s)]
> color sel byhetero
> nucleotides sel tube/slab shape box
> hide sel cartoons
> select #4,5,6,7/D
9784 atoms, 10936 bonds, 165 pseudobonds, 460 residues, 10 models selected
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select #4,5,6,7/C
1886 atoms, 2106 bonds, 93 residues, 4 models selected
> select #4,5,6,7/C
1886 atoms, 2106 bonds, 93 residues, 4 models selected
> select #4,5,6,7/B
2636 atoms, 2945 bonds, 129 residues, 4 models selected
> hide sel cartoons
> select clear
> select #1/D:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #3 models
> show #2 models
> show #1 models
> hide #2 models
> hide #!7 models
> hide #!5 models
> save "/Users/npd1/Desktop/Session 1.cxs"
> select #1,3,4,6
38329 atoms, 39780 bonds, 166 pseudobonds, 4194 residues, 8 models selected
> cartoon style (#1,3#!4,6 & sel) modeHelix tube sides 20
> cartoon style (#1,3#!4,6 & sel & coil) xsection oval
> cartoon style (#1,3#!4,6 & sel) xsection barbell modeHelix default
> cartoon style (#1,3#!4,6 & sel) modeHelix tube sides 20
> select #6/B:1-30
614 atoms, 686 bonds, 30 residues, 1 model selected
> select #6/C:1-12
245 atoms, 273 bonds, 12 residues, 1 model selected
> select #6/B:1-30
614 atoms, 686 bonds, 30 residues, 1 model selected
> select #1,3,4,6/B
1288 atoms, 1439 bonds, 63 residues, 2 models selected
> color sel white
> color sel byhetero
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> select #1/D:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #3 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> show #!4 models
> show #3 models
> save "/Users/npd1/Desktop/Session 2.cxs"
——— End of log from Tue Dec 17 15:14:27 2024 ———
opened ChimeraX session
> select #4,6/B,C,D
6972 atoms, 7791 bonds, 131 pseudobonds, 332 residues, 5 models selected
> hide sel cartoons
> hide sel atoms
> select #4,6/A
15515 atoms, 15827 bonds, 5 pseudobonds, 1912 residues, 4 models selected
> hide sel atoms
> show sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
[Repeated 2 time(s)]
> select #1,3/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel surfaces
> select #1/D:119@CA
1 atom, 1 residue, 1 model selected
> hide #!1 models
> hide #!4 models
> hide #!6 models
> select #3/D
Nothing selected
> select #3/A
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> hide sel atoms
> show #!1 models
> show #!4 models
> show #!6 models
> select #3,4,6/A
23436 atoms, 23908 bonds, 5 pseudobonds, 2887 residues, 5 models selected
> select #3,4,6/A:768,856,764,904955
99 atoms, 90 bonds, 9 residues, 3 models selected
> save "/Users/npd1/Desktop/Session 3 surfaces.cxs"
> select #3,4,6/A:768,856,764,904,955
159 atoms, 144 bonds, 15 residues, 3 models selected
> select #3,4,6/A:768,856,764,904,955,898
186 atoms, 168 bonds, 18 residues, 3 models selected
> color (#!3-4,6 & sel) red
> select #1/D:768,856,764,904,955,898
62 atoms, 56 bonds, 6 residues, 1 model selected
> color (#!1 & sel) red
> select #1/D:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) hot pink
> select #3,4,6/A:808
29 atoms, 26 bonds, 3 residues, 3 models selected
> select #3,4,6/A:808
29 atoms, 26 bonds, 3 residues, 3 models selected
> color (#!3-4,6 & sel) magenta
> save "/Users/npd1/Desktop/Session 3a surfaces.cxs"
——— End of log from Tue Dec 17 16:34:16 2024 ———
opened ChimeraX session
> select #3,4,6/A:191-340
3522 atoms, 3597 bonds, 450 residues, 3 models selected
> hide sel surfaces
> select #1/D:191-340
1174 atoms, 1199 bonds, 150 residues, 1 model selected
> hide sel surfaces
> hide #!3 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!6 models
> select #3,4,6/A:808
29 atoms, 26 bonds, 3 residues, 3 models selected
> color (#!3-4,6 & sel) magenta
> select #1/D:808
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) magenta
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save /Users/npd1/Desktop/image1.png supersample 3
> hide #!1 models
> show #!4 models
> save /Users/npd1/Desktop/image2.png supersample 3
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> save /Users/npd1/Desktop/image1.png supersample 3
> hide #!6 models
> show #!3 models
> save /Users/npd1/Desktop/image2.png supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!4 models
> select #3,4,6/B,C
2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected
> show sel & #!4 cartoons
> show #!6 models
> select #3,4,6/B,C
2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected
> show sel cartoons
> save "/Users/npd1/Desktop/Session 3b surfaces.cxs"
> hide #!6 models
> select clear
> select #3,4,6/B,C
2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected
> show #!6 models
> select #3,4,6/B,C
2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected
> nucleotides sel stubs
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> select clear
> hide #!6 models
> show #!6 models
> select #3,4,6/B,C
2080 atoms, 2323 bonds, 26 pseudobonds, 102 residues, 3 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2080 atom styles
> nucleotides sel ladder
[Repeated 1 time(s)]
> nucleotides sel tube/slab shape box
> select #6/A:887@CD
1 atom, 1 residue, 1 model selected
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save /Users/npd1/Desktop/image1.png supersample 3
> hide #!6 models
> show #!4 models
> save /Users/npd1/Desktop/image2.png supersample 3
> show #!1 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> save /Users/npd1/Desktop/image1.png supersample 3
> hide #!1 models
> show #!3 models
> hide #!4 models
> show #!6 models
> select #6/A
7729 atoms, 7884 bonds, 3 pseudobonds, 952 residues, 2 models selected
> hide sel surfaces
> save /Users/npd1/Desktop/image1.png supersample 3
Unsupported scale factor (0.000000) detected on Display0
[Repeated 1 time(s)]
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> select #3/A
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> select #3/D
Nothing selected
> select #3/A
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> select #3/A:1-60
470 atoms, 474 bonds, 57 residues, 1 model selected
> color (#!3 & sel) cornflower blue
> select #3/A:60-100,191-340
1512 atoms, 1543 bonds, 191 residues, 1 model selected
> color (#!3 & sel) yellow
> select #3/A:100-191
727 atoms, 743 bonds, 92 residues, 1 model selected
> color (#!3 & sel) red
> select #3/A:340-496
1316 atoms, 1345 bonds, 157 residues, 1 model selected
> color (#!3 & sel) orange
> select #3/A:643-696,750-811,918-978
1433 atoms, 1461 bonds, 177 residues, 1 model selected
> color (#!3 & sel) forest green
> select #3/A:696-760
530 atoms, 535 bonds, 65 residues, 1 model selected
> color (#!3 & sel) blue
> select #3/A:811-918
870 atoms, 883 bonds, 108 residues, 1 model selected
> color (#!3 & sel) magenta
> select #3,4,6/A:768,856,764,904,955,898
186 atoms, 168 bonds, 18 residues, 3 models selected
> color (#!3,6 & sel) red
> select #3,4,6/A:808
29 atoms, 26 bonds, 3 residues, 3 models selected
> color (#!3,6 & sel) purple
> select #3,4,6/A:756,659,922
55 atoms, 46 bonds, 9 residues, 3 models selected
> color (#!3,6 & sel) light sea green
> color (#!3,6 & sel) yellow
> select #3,4,6/A:922
18 atoms, 15 bonds, 3 residues, 3 models selected
> hide #!3 models
> hide #!6 models
> show #!4 models
> show #!1 models
> select #1/D:756,659,922
25 atoms, 22 bonds, 3 residues, 1 model selected
> color (#!1 & sel) yellow
> select clear
> save /Users/npd1/Desktop/image1.png supersample 3
> show #!6 models
> show #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #3/A:808@NH2
1 atom, 1 residue, 1 model selected
> ui tool show Distances
> select add #3/A:756@OE1
2 atoms, 2 residues, 2 models selected
> distance #3/A:808@NH2 #3/A:756@OE1
Distance between X2-Max 7WAZ (state II).pdb #3/A ARG 808 NH2 and GLU 756 OE1:
10.332Å
> hide #!6 models
> hide #!3 models
> show #!4 models
> show #!1 models
> select #1/D:756@OE1
1 atom, 1 residue, 1 model selected
> select add #1/D:808@NH2
2 atoms, 2 residues, 2 models selected
> distance #1/D:756@OE1 #1/D:808@NH2
Distance between X2-Max 7WAY (state I).pdb #1/D GLU 756 OE1 and ARG 808 NH2:
9.723Å
> save "/Users/npd1/Desktop/Session 4 surfaces.cxs"
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select #1/D:26,610
22 atoms, 20 bonds, 2 residues, 1 model selected
> color (#!1 & sel) red
> select #4
11453 atoms, 12041 bonds, 6 pseudobonds, 1135 residues, 3 models selected
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel surfaces
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> color (#!4 & sel) cornflower blue
> hide #!1 models
> select #4/A:26,610
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!4 & sel) red
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> sequence chain #4/C
Alignment identifier is 4/C
> select #4/C:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:6-9
79 atoms, 86 bonds, 4 residues, 1 model selected
> select #4/C:8
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:8-10
60 atoms, 66 bonds, 3 residues, 1 model selected
> select clear
> select #4/B:-2-0
60 atoms, 66 bonds, 3 residues, 1 model selected
> select #4/C:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:7-9
59 atoms, 64 bonds, 3 residues, 1 model selected
> select #4/C:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/C:7-10
80 atoms, 88 bonds, 4 residues, 1 model selected
> color sel hot pink
> save /Users/npd1/Desktop/T26-K610.cxs
> select #4/A:562-568
52 atoms, 51 bonds, 7 residues, 1 model selected
> select #4/A:561-568
60 atoms, 59 bonds, 8 residues, 1 model selected
> hide sel surfaces
> undo
> select #4/A:561-568
60 atoms, 59 bonds, 8 residues, 1 model selected
> show sel surfaces
> select #4/A:562-568
52 atoms, 51 bonds, 7 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select #4/A:563-568
43 atoms, 42 bonds, 6 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select #4/A:564-568
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #4/A:563-568
43 atoms, 42 bonds, 6 residues, 1 model selected
> select #4/A:562-568
52 atoms, 51 bonds, 7 residues, 1 model selected
> hide sel surfaces
> select #4/A:26,610
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!4 & sel) magenta
> select #4/A:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!4 & sel) orange
> select #4/A:610@CD
1 atom, 1 residue, 1 model selected
> select #4/A:603@CA
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/npd1/Desktop/image2.png supersample 3
> save /Users/npd1/Desktop/image3.png supersample 3
> select #4/A:562-568
52 atoms, 51 bonds, 7 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> transparency (#!4 & sel) 80
> hide sel surfaces
> save /Users/npd1/Desktop/image4.png supersample 3
> show #!1 models
> select #1/D:562-568
52 atoms, 51 bonds, 7 residues, 1 model selected
> hide sel surfaces
> select #4/A:26,610
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!4 & sel) magenta
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show sel surfaces
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) magenta
> select #1/D:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) orange
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> hide sel surfaces
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> select #1/D:562-568
52 atoms, 51 bonds, 7 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select #1/D:563-568
43 atoms, 42 bonds, 6 residues, 1 model selected
> select #1/D:563-567
36 atoms, 35 bonds, 5 residues, 1 model selected
> hide sel surfaces
> select #1/D:563
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #1/D:564
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #1/D:565
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #1/D:566
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #1/D:567
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #1/D:568
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #1/D:569
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:561
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:562
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/D:563
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #1/D:564
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show sel surfaces
> select #1/D:191:340
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/D:191:340
17 atoms, 15 bonds, 2 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> select #1/D:191:340
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> select #1/D:191-340
1174 atoms, 1199 bonds, 150 residues, 1 model selected
> hide sel surfaces
> lighting soft
> lighting full
> lighting simple
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select #1/D:26,610
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select #4/B,C
1221 atoms, 1364 bonds, 60 residues, 1 model selected
> hide sel cartoons
> color sel byhetero
> select #1/D:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) forest green
> color sel byhetero
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show sel surfaces
> select #1/D:26,610
22 atoms, 20 bonds, 2 residues, 1 model selected
> transparency (#!1 & sel) 70
> select #1/D:563
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 70
> show sel atoms
> select #4/C,D
2993 atoms, 3345 bonds, 1 pseudobond, 142 residues, 2 models selected
> show sel cartoons
> select #4/B,C
1221 atoms, 1364 bonds, 60 residues, 1 model selected
> show sel cartoons
> select #1/D:25@CA
1 atom, 1 residue, 1 model selected
> select #1/D:26@NH2
1 atom, 1 residue, 1 model selected
> select #1/D:191@NE2
1 atom, 1 residue, 1 model selected
> select #1/D:642@O
1 atom, 1 residue, 1 model selected
> select #1/D:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 70
> show sel cartoons
> show sel atoms
> select #1/D:642@NH1
1 atom, 1 residue, 1 model selected
> select clear
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 0
> color (#!1 & sel) cornflower blue
> select clear
> save /Users/npd1/Desktop/image5.png supersample 3
> hide #!1 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel surfaces
> color (#!4 & sel) cornflower blue
> select #4/A:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:26,25,563
25 atoms, 23 bonds, 3 residues, 1 model selected
> transparency (#!4 & sel) 70
> show sel atoms
> select #4/A:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 4 time(s)]
> color (#!4 & sel) forest green
> color sel byhetero
> select #4/A:613@ND2
1 atom, 1 residue, 1 model selected
Drag select of 7way (CasX2 state I).pdb_A SES surface, 186 of 1019076
triangles
> select #4/A:195-400
1652 atoms, 1690 bonds, 206 residues, 1 model selected
> hide sel surfaces
> select #4/A:164-400
1840 atoms, 1882 bonds, 1 pseudobond, 229 residues, 2 models selected
> hide sel surfaces
> select #4/A:132-400
2102 atoms, 2151 bonds, 1 pseudobond, 261 residues, 2 models selected
> select #4/A:99-400
2298 atoms, 2350 bonds, 2 pseudobonds, 287 residues, 2 models selected
> hide sel surfaces
> hide #!4 models
> show #!4 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel atoms
> select #4/A:99-400
2298 atoms, 2350 bonds, 2 pseudobonds, 287 residues, 2 models selected
> hide sel atoms
> select #4/A:98-400
2304 atoms, 2356 bonds, 2 pseudobonds, 288 residues, 2 models selected
> hide sel surfaces
> hide sel atoms
> select #4/A:8-400
3042 atoms, 3106 bonds, 2 pseudobonds, 378 residues, 2 models selected
> hide sel atoms
> undo
> select #4/A:88-400
2384 atoms, 2438 bonds, 2 pseudobonds, 298 residues, 2 models selected
> hide sel surfaces
> hide sel atoms
> save /Users/npd1/Desktop/image6.png supersample 3
> select #4/A:563
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!4 & sel) 0
> select #4/A:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!4 & sel) 0
> select clear
> select #4/A:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency (#!4 & sel) 80
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting simple
> lighting shadows true
> lighting simple
> save /Users/npd1/Desktop/image7.png supersample 3
> select clear
> save /Users/npd1/Desktop/image8.png supersample 3
> save /Users/npd1/Desktop/T26.cxs
——— End of log from Wed Dec 18 17:53:52 2024 ———
opened ChimeraX session
> select #4/D
2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 2446 atom styles
> nucleotides sel ladder
[Repeated 3 time(s)]
> show sel atoms
> nucleotides sel ladder
[Repeated 1 time(s)]
> nucleotides sel tube/slab shape box
> select #4/A:28@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> select #4/A:85
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel surfaces
> select #4/D
2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected
> color (#!4 & sel) orange
> select #4/A:29@CG
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/npd1/Desktop/image11.png supersample 3
> save /Users/npd1/Desktop/T26a.cxs
——— End of log from Wed Dec 18 18:16:40 2024 ———
opened ChimeraX session
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> select #4/A:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> transparency (#!4 & sel) 0
> color (#!4 & sel) cornflower blue
> select #4/A:610
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!4 & sel) 80
> color (#!4 & sel) forest green
> color sel byhetero
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel surfaces
> select #4/A:613@CB
1 atom, 1 residue, 1 model selected
> select #4/A:643@CB
1 atom, 1 residue, 1 model selected
> select #4/A:22@CD
1 atom, 1 residue, 1 model selected
> select #4/A:24@CA
1 atom, 1 residue, 1 model selected
> select #1
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> save /Users/npd1/Desktop/image1.png supersample 3
> save /Users/npd1/Desktop/K610.cxs
——— End of log from Thu Dec 19 08:04:12 2024 ———
opened ChimeraX session
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show #!4 atoms
> show #!4 surfaces
> select #4/B,C,D
3667 atoms, 4098 bonds, 1 pseudobond, 175 residues, 2 models selected
> hide sel surfaces
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show #!1 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> transparency (#!4 & sel) 0
> select #4/D
2446 atoms, 2734 bonds, 1 pseudobond, 115 residues, 2 models selected
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> transparency (#!1 & sel) 0
> select #1/D:26
11 atoms, 10 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 80
> save /Users/npd1/Desktop/R610.cxs
> select #1/D:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/D:563
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 80
> select #1/D:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 80
> show sel surfaces
> select clear
> save /Users/npd1/Desktop/R610.cxs
> save /Users/npd1/Desktop/image2.png supersample 3
> select #1/D:25,563
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel byhetero
> hide sel surfaces
> show sel surfaces
> select clear
[Repeated 1 time(s)]
> save /Users/npd1/Desktop/R610.cxs
——— End of log from Thu Dec 19 08:17:31 2024 ———
opened ChimeraX session
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> transparency (#!1 & sel) 0
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> transparency (#!1 & sel) 80
> color (#!1 & sel) forest green
> color sel byhetero
> ui tool show Rotamers
Populating font family aliases took 70 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> swapaa interactive sel ARG rotLib Dunbrack
X2-Max 7WAY (state I).pdb #1/D ARG 610: phi -126.4, psi 147.2 trans
Changed 600 bond radii
> select up
123 atoms, 123 bonds, 15 residues, 2 models selected
> save /Users/npd1/Desktop/R610.cxs
——— End of log from Thu Dec 19 08:48:26 2024 ———
opened ChimeraX session
> select #1/D:563-564
15 atoms, 14 bonds, 2 residues, 1 model selected
> transparency (#!1 & sel) 80
> ui tool show Rotamers
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B
674 atoms, 753 bonds, 33 residues, 1 model selected
> hide sel cartoons
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
X2-Max 7WAY (state I).pdb #1/D ARG 610: phi -126.4, psi 147.2 trans
Changed 600 bond radii
> select #1.2.23/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #!1/D:563@CE
2 atoms, 2 residues, 2 models selected
> select add #4/B:22@OP1
3 atoms, 3 residues, 4 models selected
> select #1.2.48/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #1.2.23/A:1@NH2
2 atoms, 2 residues, 2 models selected
> select #1.2.23/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #1.2.23/A:1@NH2 #4/B:22@OP1
Distance between rotamer 23 #1.2.23/A ARG 1 NH2 and 7way (CasX2 state I).pdb
#4/B DG 22 OP1: 2.632Å
> distance #1.2.23/A:1@NH2 #4/B:22@OP1
Distance already exists; modify distance properties with 'distance style'
> select #1.2.57/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #1.2.57/A:1@NH2 #4/B:22@OP1
Distance between rotamer 57 #1.2.57/A ARG 1 NH2 and 7way (CasX2 state I).pdb
#4/B DG 22 OP1: 2.451Å
> select #1.2.48/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #1.2.48/A:1@NH2 #4/B:22@OP1
Distance between rotamer 48 #1.2.48/A ARG 1 NH2 and 7way (CasX2 state I).pdb
#4/B DG 22 OP1: 2.329Å
> swapaa #!1/D:610 ARG criteria 48 rotLib Dunbrack retain false
Using Dunbrack library
X2-Max 7WAY (state I).pdb #!1/D ARG 610: phi -126.4, psi 147.2 trans
Applying ARG rotamer (chi angles: -170.4 -85.5 -170.4 -173.1) to X2-Max 7WAY
(state I).pdb #!1/D ARG 610
> select #1/D:612
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel surfaces
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> hide sel surfaces
> select #1/D:611
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/D:612
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/D:611
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
X2-Max 7WAY (state I).pdb #1/D ARG 610: phi -126.4, psi 147.2 trans
Changed 600 bond radii
Drag select of 1 atoms, 1 residues
> select #1.2.57/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #1.2.57/A:1@NH2 #4/B:22@OP1
Distance between rotamer 57 #1.2.57/A ARG 1 NH2 and 7way (CasX2 state I).pdb
#4/B DG 22 OP1: 2.453Å
> select #1.2.23/A:1@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #1.2.23/A:1@NH2 #4/B:22@OP1
Distance between rotamer 23 #1.2.23/A ARG 1 NH2 and 7way (CasX2 state I).pdb
#4/B DG 22 OP1: 2.633Å
> swapaa #!1/D:610 ARG criteria 23 rotLib Dunbrack retain false
Using Dunbrack library
X2-Max 7WAY (state I).pdb #!1/D ARG 610: phi -126.4, psi 147.2 trans
Applying ARG rotamer (chi angles: -178.6 176.8 -178.6 -89.1) to X2-Max 7WAY
(state I).pdb #!1/D ARG 610
> select #1/D
7921 atoms, 8081 bonds, 1 pseudobond, 975 residues, 2 models selected
> show sel surfaces
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel surfaces
> select #1/D:610@NH2
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 3 models selected
> distance #1/D:610@NH2 #4/B:22@OP1
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH2 and 7way (CasX2
state I).pdb #4/B DG 22 OP1: 2.633Å
> show #!8 models
> ~distance #1/D:610@NH2 #4/B:22@OP1
> ~distance #1/D:26@NH2 #4/B:21@OP1
> ~distance #3/A:26@NH2 #4/C:11@O2
> ~distance #3/A:26@NH2 #4/B:20@OP1
> ~distance #1/D:26@NH2 #3/A:26@NH2
> ~distance #4/A:610@NZ #4/B:22@OP1
> ~distance #4/B:20@OP1 #1/D:26@NH2
> ~distance #3/A:610@NH1 #4/B:22@OP1
> ~distance #3/A:808@NH1 #6/B:3@OP1
> ~distance #1/D:26@NH2 #4/B:20@OP2
> ~distance #4/C:21@OP2 #1/D:808@NH1
> ~distance #6/A:610@NZ #6/B:22@OP1
> ~distance #1/D:808@NH2 #4/C:21@OP2
> ~distance #6/B:21@OP1 #2/D:26@NH2
> ~distance #4/A:610@NZ #4/B:21@OP2
> ~distance #2/D:26@NH2 #6/B:21@OP2
> ~distance #2/D:610@NH1 #6/B:21@OP2
> ~distance #6/A:808@NZ #6/B:3@OP1
> ~distance #2/D:610@NH1 #6/B:22@OP1
> ~distance #3/A:26@NH2 #4/B:21@OP2
> ~distance #6/B:20@OP1 #2/D:26@NH2
> ~distance #3/A:26@NH2 #6/C:11@O2
> ~distance #6/A:610@NZ #6/B:21@OP2
> ~distance #3/A:26@NH2 #6/B:20@OP1
> ~distance #3/A:26@NH2 #6/B:21@OP1
> ~distance #1/D:26@NH2 #2/D:26@NH2
> ~distance #6/A:610@NZ #2/D:610@NH1
> ~distance #1/D:26@NH2 #4/C:12@O2
> ~distance #3/A:26@NH1 #6/B:21@OP1
> ~distance #4/A:808@NZ #4/C:21@OP2
> ~distance #2/D:26@NH2 #6/C:12@O2
> ~distance #3/A:26@NH2 #6/C:12@O2
> ~distance #3/A:808@NH2 #6/B:3@OP1
> ~distance #1/D:756@OE1 #1/D:808@NH2
> ~distance #3/A:808@NH2 #3/A:756@OE1
> ~distance #3/A:26@NH2 #4/B:20@OP2
> ~distance #3/A:26@NH2 #4/B:21@OP1
> ~distance #1/D:26@NH2 #4/C:11@O2
> ~distance #1/D:26@NH2 #4/B:21@OP2
> ui tool show Distances
> distance #1/D:610@NH2 #4/B:22@OP1
Distance between X2-Max 7WAY (state I).pdb #1/D ARG 610 NH2 and 7way (CasX2
state I).pdb #4/B DG 22 OP1: 2.633Å
> select #1/D:608@CA
1 atom, 1 residue, 1 model selected
> select #2
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> save /Users/npd1/Desktop/R610.cxs
> save /Users/npd1/Desktop/image7.png supersample 3
> hide #!1 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel surfaces
> select #4/A:610
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> select #4/A:610@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:22@OP1
2 atoms, 2 residues, 2 models selected
> distance #4/A:610@NZ #4/B:22@OP1
Distance between 7way (CasX2 state I).pdb #4/A LYS 610 NZ and /B DG 22 OP1:
4.707Å
> show sel surfaces
> hide sel surfaces
> select #4/A:610
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> transparency (#!4 & sel) 80
> save /Users/npd1/Desktop/K610.cxs
> select clear
> save /Users/npd1/Desktop/image8.png supersample 3
> save /Users/npd1/Desktop/K610a.cxs
> show #!1 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 80
> select clear
> save /Users/npd1/Desktop/R610a.cxs
——— End of log from Thu Dec 19 09:27:48 2024 ———
opened ChimeraX session
> select #4/A:563-4
Nothing selected
> select #1/D:563-4
Nothing selected
> select #1/D:563-564
15 atoms, 14 bonds, 2 residues, 1 model selected
> transparency (#!1 & sel) 80
> select #1/D:227@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #1/D:563-566
28 atoms, 27 bonds, 4 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #1/D:562-566
37 atoms, 36 bonds, 5 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:22-26
38 atoms, 37 bonds, 5 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:561-566
45 atoms, 44 bonds, 6 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:561-566,642
56 atoms, 54 bonds, 7 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:561-566,640-642
76 atoms, 74 bonds, 9 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #1/D:561-566,640-642,509
87 atoms, 85 bonds, 10 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:561-566,640-642,509,610
98 atoms, 95 bonds, 11 residues, 1 model selected
> hide sel surfaces
> select #1/D:561-566,640-642,509
87 atoms, 85 bonds, 10 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> transparency (#!1 & sel) 0
> select #1/D:64@CG
1 atom, 1 residue, 1 model selected
> select #1/D:640-642
31 atoms, 30 bonds, 3 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:640-642,563
40 atoms, 38 bonds, 4 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/D:509
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> select #1/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> select #1/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> transparency (#!1 & sel) 0
> hide sel surfaces
> hide sel atoms
> select #1/D:610
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> select #1/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> label height 3
> label height 2
> label height 1
> select clear
> label size 1000
> label size 1
> label size 20
> label size 30
> label size 40
> label size 2.5
Invalid "size" argument: Expected 'default' or an integer
> label size 3
> label size 2
> label size 40
> label height 3
> label height 2.5
> label height 2
> label height 1.5
> label height 1
> label height 1.25
> select clear
> save /Users/npd1/Desktop/image5.png supersample 3
> save /Users/npd1/Desktop/R610b.cxs
——— End of log from Thu Dec 19 14:32:51 2024 ———
opened ChimeraX session
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> select #1/D
7921 atoms, 8081 bonds, 975 residues, 1 model selected
> cartoon style (#!1 & sel) xsection oval modeHelix default
> label size 1
> label label height 1
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label height 1
> label height 0
> select clear
> save /Users/npd1/Desktop/image1.png supersample 3
> save /Users/npd1/Desktop/image2.png supersample 3
> hide #!1 models
> select #4/A
7786 atoms, 7943 bonds, 2 pseudobonds, 960 residues, 2 models selected
> show sel cartoons
> cartoon style (#!4 & sel) xsection oval modeHelix default
> select #4/A:610
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/npd1/Desktop/image3.png supersample 3
> save /Users/npd1/Desktop/K610c.cxs
——— End of log from Fri Dec 20 14:41:34 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MC8N4LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.120.111.0.1
OS Loader Version: 11881.120.111.0.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F5053f)
Kernel Version: Darwin 24.5.0
Time since boot: 8 hours, 23 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Display:
Resolution: 2560 x 1600
UI Looks like: 2560 x 1600 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
VX3276-FHD:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report dialog explained what we know about this crash
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
The current ChimeraX daily build uses a newer Qt version 6.8.2 and we have not observed these Mac multi-display crashes using it. So you might want to try the ChimeraX daily build.
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Reported by Niles Donegan