![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8359 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
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"procLaunch" : "2023-01-20 13:38:16.3909 -0800",
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"captureTime" : "2023-01-20 14:18:00.3365 -0800",
"incident" : "6E0ED359-35B1-41F4-A95D-7C40DD76821C",
"bug_type" : "309",
"pid" : 14494,
"procExitAbsTime" : 47813710999855,
"cpuType" : "X86-64",
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"name" : "CoreFoundation",
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Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0152, step 1, values float32
Log from Fri Jan 20 15:36:51 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.0152, step 1, values float32
Log from Mon Jan 16 15:41:27 2023
> lighting soft
> set bgColor white
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_19/NEC_011123_2_RSR_015_Arg474_real_space_refined_019.pdb
Chain information for NEC_011123_2_RSR_015_Arg474_real_space_refined_019.pdb
#1
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_21/01123_real_space_refined_021.pdb
Chain information for 01123_real_space_refined_021.pdb #2
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_22/01123_real_space_refined_022.pdb
Chain information for 01123_real_space_refined_022.pdb #3
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open /Users/amberms/Desktop/group/Modeling/122122/01123.pdb
Summary of feedback from opening
/Users/amberms/Desktop/group/Modeling/122122/01123.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
23743 messages similar to the above omitted
Chain information for 01123.pdb #4
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide atoms
> show cartoons
> select #1:A:402,411,412,414,471,474,478,481
517 atoms, 525 bonds, 24 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select #1/A:402,411,412,414,471,474,478,481
124 atoms, 120 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 124 atom styles
> color sel yellow
> select #1/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 135 atom styles
> style sel ball
Changed 135 atom styles
> color sel yellow
> select #A/C:402,411,412,414,471,474,478,481
Expected an objects specifier or a keyword
> show #!2 models
> show #!3 models
> show #!4 models
> select #2/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel cyan
> select #2/A:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel cyan
> select #3/A:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff9300ff
> select #3/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff2600ff
> color sel #ff9300ff
> select #4/A:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff2f92ff
> select #4/C:402,411,412,414,471,474,478,481
135 atoms, 131 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 135 atom styles
> color sel #ff40ffff
> color sel #ff2f92ff
> select clear
> select H
75541 atoms, 9172 residues, 4 models selected
> hide sel target a
> hide sel cartoons
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!1 models
> color sel byhetero
> color sel byhetero
> color sel byhetero
> select #1,2,3,4/A,C:402,411,412,414,471,474,478,481
1069 atoms, 1037 bonds, 64 residues, 4 models selected
> color sel byhetero
> select clear
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!2 cartoons
> show #!4 models
> show #!2,4 cartoons
> hide #!4 models
> show #!4 models
> open
> /Users/amberms/Desktop/group/Modeling/122122/cryosparc_P183_J130_locfilter_flip.mrc
Opened cryosparc_P183_J130_locfilter_flip.mrc as #5, grid size 220,220,220,
pixel 1.67, shown at level 0.00879, step 1, values float32
> volume #5 level 0.01524
> lighting soft
> transparency 50
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!2 cartoons
> graphics silhouettes true
> ui tool show Distances
> select add #2/A:474@NH1
1 atom, 1 residue, 1 model selected
> select add #2/A:478@OE1
2 atoms, 2 residues, 1 model selected
> distance #2/A:474@NH1 #2/A:478@OE1
Distance between 01123_real_space_refined_021.pdb #2/A ARG 474 NH1 and GLU 478
OE1: 2.424Å
> select clear
> select add #2/A:474@NE
1 atom, 1 residue, 1 model selected
> select add #2/A:471@OD1
2 atoms, 2 residues, 1 model selected
> distance #2/A:474@NE #2/A:471@OD1
Distance between 01123_real_space_refined_021.pdb #2/A ARG 474 NE and ASP 471
OD1: 3.466Å
> select clear
> select add #2/A:471@OD1
1 atom, 1 residue, 1 model selected
> select add #2/A:474@NH2
2 atoms, 2 residues, 1 model selected
> distance #2/A:471@OD1 #2/A:474@NH2
Distance between 01123_real_space_refined_021.pdb #2/A ASP 471 OD1 and ARG 474
NH2: 3.419Å
> select clear
> select add #2/C:474@NH2
1 atom, 1 residue, 1 model selected
> select add #2/C:478@OE2
2 atoms, 2 residues, 1 model selected
> distance #2/C:474@NH2 #2/C:478@OE2
Distance between 01123_real_space_refined_021.pdb #2/C ARG 474 NH2 and GLU 478
OE2: 3.263Å
> select clear
> select add #2/C:474@NH1
1 atom, 1 residue, 1 model selected
> select add #2/C:478@OE2
2 atoms, 2 residues, 1 model selected
> distance #2/C:474@NH1 #2/C:478@OE2
Distance between 01123_real_space_refined_021.pdb #2/C ARG 474 NH1 and GLU 478
OE2: 4.710Å
> select clear
> select add #2/C:471@OD1
1 atom, 1 residue, 1 model selected
> select add #2/C:474@NH1
2 atoms, 2 residues, 1 model selected
> distance #2/C:471@OD1 #2/C:474@NH1
Distance between 01123_real_space_refined_021.pdb #2/C ASP 471 OD1 and ARG 474
NH1: 5.085Å
> show #!1 models
> hide #!1 models
> select clear
> select add #2/C:471@OD1
1 atom, 1 residue, 1 model selected
> select add #2/A:474@NE
2 atoms, 2 residues, 1 model selected
> distance #2/C:471@OD1 #2/A:474@NE
Distance between 01123_real_space_refined_021.pdb #2/C ASP 471 OD1 and /A ARG
474 NE: 5.557Å
> distance style symbol false
> distance style symbol true
> show sel cartoons
> hide #!6 models
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/E
Alignment identifier is 2/E
> hide #!2 models
> show #!2 models
> select #2
40815 atoms, 41357 bonds, 7 pseudobonds, 2637 residues, 2 models selected
> show sel cartoons
> select clear
> show #!5 models
> show #!3 models
> show #!2-3 cartoons
> hide #!5 models
> show #!4 models
> hide #6.1 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2-4 cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!4 models
> select add #2/C:471@CG
1 atom, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ASP rotLib Dunbrack
01123_real_space_refined_021.pdb #2/C ASP 471: phi -62.9, psi -41.8 trans
Changed 90 bond radii
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> hide sel atoms
> select clear
> hide #!2 atoms
> show #!2 cartoons
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #ff2f92ff
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #531b93ff
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #009193ff
> select clear
> show #!5 models
> color zone #5 near #2 distance 5
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #531b93ff
> hide #!5 models
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #ff2f92ff
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdffff
> select clear
> show #!5 models
> color zone #5 near #2 distance 5
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!5 models
> save "/Users/amberms/Desktop/NEC Paper/figures/figure1B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure_1
> view list
Named views: figure_1
> view figure_1
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdff33
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #00fdff05
> color sel #00fdff33
> color sel #ff2f92ff
> color sel #ff2f9233
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #531b93ff
> color sel #531b9333
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> color sel #ff930033
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> show sel atoms
> style sel ball
Changed 246 atom styles
> color (#!2 & sel) #fffb00ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #0433ffff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #00f900ff
> color (#!2 & sel) #8efa00ff
> color (#!2 & sel) #00f900ff
> color sel byhetero
> select H
75541 atoms, 9172 residues, 4 models selected
> hide (#!2 & sel) target a
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> color (#!2 & sel) #a9a9a9ff
> color (#!2 & sel) #a9a9a933
> color (#!2 & sel) #a9a9a900
> color (#!2 & sel) #a9a9a980
> color (#!2 & sel) #a9a9a9b3
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #00f900ff
> color sel byhetero
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #009193ff
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #005493ff
> color (#!2 & sel) #fffb00ff
> select #2/B,E,D,H, G
6681 atoms, 6871 bonds, 537 residues, 1 model selected
> hide sel cartoons
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color sel byhetero
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #fffc79ff
> color (#!2 & sel) #fffb00ff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #fffb00ff
> color sel byhetero
> select #2/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 24 atom styles
> select H
75541 atoms, 9172 residues, 4 models selected
> hide (#!2 & sel) target a
> select #2/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> color sel #00fa92ff
> color sel #00fdffff
> color sel byhetero
> select clear
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select #2/A,C:402,411,412,414,474,478,481,471
270 atoms, 262 bonds, 7 pseudobonds, 16 residues, 2 models selected
> graphics silhouettes true
> select clear
> view name figure_2a
> view list
Named views: figure_1, figure_2a
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A.png" width 1704
> height 1146 supersample 3
> show #!5 models
> transparency 50
> hide #!5 models
> show #!5 models
> transparency 90
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> color (#!2 & sel) #929292ff
> color (#!2 & sel) #a9a9a9ff
> select clear
> select #2/A,C:402,411,412,414,474,478,481
246 atoms, 240 bonds, 3 pseudobonds, 14 residues, 2 models selected
> color (#!2 & sel) #fffb00ff
> color sel byhetero
> select #2/A,C:471
24 atoms, 22 bonds, 2 residues, 1 model selected
> color sel #0096ffff
> color sel #00fdffff
> color sel byhetero
> select clear
> view name figure_2b
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2A_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure_2c
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> transparency 70
> transparency 80
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure2B.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!5 models
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
> show #!2 cartoons
> hide #!2 atoms
> select #2/A,C
34134 atoms, 34486 bonds, 7 pseudobonds, 2100 residues, 2 models selected
> color (#!2 & sel) #a9a9a9ff
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color sel #ff2f92ff
> select #2/E
1335 atoms, 1347 bonds, 78 residues, 1 model selected
> color sel #531b93ff
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #0096ffff
> color sel #00fdffff
> select clear
> select #2/D,H,E,B,G
6681 atoms, 6871 bonds, 537 residues, 1 model selected
> hide sel cartoons
> open 5DIS
Summary of feedback from opening 5DIS fetched from pdb
---
warnings | Unknown polymer entity '6' near line 18113
Atom OXT is not in the residue template for PRO /C:301
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
5dis title:
Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino
acid FG-repeat containing fragment of Nup214 [more info...]
Chain information for 5dis #7
---
Chain | Description
A | Exportin-1
B | GTP-binding nuclear protein Ran
C | Snurportin-1
D | Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214
Non-standard residues in 5dis #7
---
GLC — alpha-D-glucopyranose
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> mmaker #7/A to #2/A
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 01123_real_space_refined_021.pdb, chain A (#2) with 5dis, chain A
(#7), sequence alignment score = 5346.9
RMSD between 980 pruned atom pairs is 0.691 angstroms; (across all 1030 pairs:
1.266)
> select #7/B,D,C
6591 atoms, 6740 bonds, 20 pseudobonds, 843 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> hide #!2 models
> hide sel atoms
> select #7/E
23 atoms, 24 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #7/A:1101,499,491
36 atoms, 38 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> open
> /Users/amberms/Desktop/group/Modeling/122122/RealSpaceRefine_21/01123_real_space_refined_021.pdb
Chain information for 01123_real_space_refined_021.pdb #8
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> hide #!7-8 atoms
> show #!7-8 cartoons
> select #7/B,D,C
6591 atoms, 6740 bonds, 20 pseudobonds, 843 residues, 3 models selected
> hide sel cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!2 models
> show #!8 models
> hide #!2 models
> mmaker #8/C to #2/A
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 01123_real_space_refined_021.pdb, chain A (#2) with
01123_real_space_refined_021.pdb, chain C (#8), sequence alignment score =
5413.4
RMSD between 1025 pruned atom pairs is 0.435 angstroms; (across all 1050
pairs: 1.023)
> hide #!8 models
> show #!8 models
> show #!2 models
> hide #!8 models
> show #!8 models
> select #8/A,B,D,E,H,G
23748 atoms, 24114 bonds, 1587 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> select #2/C,B,D,E,H,G
23748 atoms, 24114 bonds, 3 pseudobonds, 1587 residues, 2 models selected
> hide sel cartoons
> hide #!8 models
> hide #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_5DIS.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!3 cartoons
> hide #!3 models
> show #!7 models
> view name figure_3_1
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_5DIS.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!7 models
> show #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!2 models
> show #!8 models
> show #!2 models
> hide #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!8 models
> show #!2 models
> show #!8 models
> hide #!2 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> select #8/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel yellow
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #2/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel yellow
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_Crm1A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #!8 models
> hide #!8 models
> show #!2 cartoons
> select #2/B,E,D,H,G
6681 atoms, 6871 bonds, 537 residues, 1 model selected
> hide sel cartoons
> select #2/C
17067 atoms, 17243 bonds, 3 pseudobonds, 1050 residues, 2 models selected
> color (#!2 & sel) #797979ff
> select clear
> select #2/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel yellow
> select clear
> view name figure_3_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> view name figure_3_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_dimerloops.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> show #!2 surfaces
> select #2/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> select #2/B,E,G
3885 atoms, 4007 bonds, 193 residues, 1 model selected
> hide sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
01123_real_space_refined_021.pdb #2/G A 119 O5'
01123_real_space_refined_021.pdb #2/G G 171 OP1
01123_real_space_refined_021.pdb #2/G G 171 P
01123_real_space_refined_021.pdb #2/G G 171 O5'
01123_real_space_refined_021.pdb #2/G G 171 OP2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 01123_real_space_refined_021.pdb_B SES surface #2.3:
minimum, -12.25, mean 5.44, maximum 22.90
Coulombic values for 01123_real_space_refined_021.pdb_E SES surface #2.6:
minimum, -8.00, mean 3.96, maximum 20.57
Coulombic values for 01123_real_space_refined_021.pdb_G SES surface #2.7:
minimum, -28.79, mean -14.78, maximum -1.19
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> coulombic #!2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 01123_real_space_refined_021.pdb_A SES surface #2.2:
minimum, -29.56, mean -1.13, maximum 19.93
Coulombic values for 01123_real_space_refined_021.pdb_B SES surface #2.3:
minimum, -12.25, mean 5.44, maximum 22.90
Coulombic values for 01123_real_space_refined_021.pdb_C SES surface #2.4:
minimum, -19.04, mean -1.19, maximum 18.78
Coulombic values for 01123_real_space_refined_021.pdb_D SES surface #2.5:
minimum, -11.36, mean 2.56, maximum 16.39
Coulombic values for 01123_real_space_refined_021.pdb_E SES surface #2.6:
minimum, -8.00, mean 3.96, maximum 20.57
Coulombic values for 01123_real_space_refined_021.pdb_G SES surface #2.7:
minimum, -28.79, mean -14.78, maximum -1.19
Coulombic values for 01123_real_space_refined_021.pdb_H SES surface #2.8:
minimum, -10.42, mean 2.57, maximum 18.49
To also show corresponding color key, enter the above coulombic command and
add key true
> select #2/B,E,G
3885 atoms, 4007 bonds, 193 residues, 1 model selected
> hide sel surfaces
> view name figure_3_3
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> view name figure_3_4
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png" width 1704
> height 1146 supersample 3
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_ES_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure_3_5
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
> hide #!2 surfaces
> select #2/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color (#!2 & sel) #00fdffff
> color (#!2 & sel) #00fdff80
> color (#!2 & sel) #00fdff00
> color (#!2 & sel) #00fdff4d
> select #2/B
1304 atoms, 1316 bonds, 76 residues, 1 model selected
> color (#!2 & sel) #ff2f92ff
> color (#!2 & sel) #ff2f924d
> select clear
> view name figure_3_6
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_RevBS.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/011623.cxs"
——— End of log from Mon Jan 16 15:41:27 2023 ———
opened ChimeraX session
> open "/Users/amberms/Desktop/NEC Paper/figures/NEC_011923.pdb"
Chain information for NEC_011923.pdb #9
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> open "/Users/amberms/Desktop/NEC Paper/figures/NEC_011923.pdb"
Chain information for NEC_011923.pdb #10
---
Chain | Description
A C | No description available
B | No description available
D H | No description available
E | No description available
G | No description available
> save "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
> hide #9-10#!2 atoms
> show #9-10#!2 cartoons
> mmaker #10/C to #9/A
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 NEC_011923.pdb, chain A (#9) with NEC_011923.pdb, chain C (#10),
sequence alignment score = 5399.6
RMSD between 1025 pruned atom pairs is 0.429 angstroms; (across all 1050
pairs: 1.010)
> hide #10 models
> hide #9 models
> hide #!2 models
> show #!7 models
> view list
Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1,
figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6
> view figure_3_2
> coulombic #!7
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
5dis #7/A GLU 1048 OXT
5dis #7/D GLY 2027 OXT
5dis #7/C GLY 287 OXT
5dis #7/B MET 179 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of 5dis #/B MET 179 H bonded to atom that should not have
hydrogens (copy of 5dis #/B MET 179 C)
> select H
132205 atoms, 16051 residues, 7 models selected
> select #7/B
1440 atoms, 1466 bonds, 6 pseudobonds, 183 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> coulombic #!7
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
5dis #7/A GLU 1048 OXT
5dis #7/D GLY 2027 OXT
5dis #7/C GLY 287 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5dis_A SES surface #7.3: minimum, -25.78, mean -2.95,
maximum 10.90
Coulombic values for 5dis_C SES surface #7.4: minimum, -32.04, mean -0.55,
maximum 10.32
Coulombic values for 5dis_D SES surface #7.5: minimum, -18.89, mean -2.55,
maximum 13.38
To also show corresponding color key, enter the above coulombic command and
add key true
> select #7/C,D
5151 atoms, 5274 bonds, 14 pseudobonds, 660 residues, 2 models selected
> hide sel surfaces
> view figure_3_2
> hide #!7 models
> select #7
13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected
> select clear
> select #7
13551 atoms, 13843 bonds, 15 pseudobonds, 1698 residues, 2 models selected
> view figure_3_3
> show #!2 models
> view list
Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1,
figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6
> view figure_3_4
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure_3_6
> show #9 models
> show #10 models
> hide #10 models
> ~select #7
3 models selected
> hide #!2 models
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #797979ff
> select #9/D,H
2796 atoms, 2864 bonds, 344 residues, 1 model selected
> color sel #ff9300ff
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color sel #531b93ff
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color sel #ff2f92ff
> select #9/G
1246 atoms, 1344 bonds, 39 residues, 1 model selected
> color sel #00fdffff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
> select #9/B
1326 atoms, 1338 bonds, 79 residues, 1 model selected
> color sel #ff2f92ff
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> color sel #531b93ff
> select clear
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #8efa00ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #fffb00ff
> select clear
> select #9/E
1349 atoms, 1361 bonds, 80 residues, 1 model selected
> select #9/E:13-26
253 atoms, 254 bonds, 14 residues, 1 model selected
> color sel #9437ffff
> color sel #7a81ffff
> color sel #531b93ff
> color sel #875093ff
> color sel #875093ff
> color sel #8f5f93ff
> color sel #8f5f93ff
> color sel #937392ff
> color sel #937392ff
> color sel #835b93ff
> color sel #835b93ff
> color sel #935b90ff
> color sel #935b90ff
> color sel #934f81ff
> color sel #934f81ff
> color sel #936791ff
> color sel #936791ff
> select #9/E:51-60
171 atoms, 171 bonds, 10 residues, 1 model selected
> color sel #011993ff
> color sel #936791ff
> select clear
> view list
Named views: figure_1, figure_2a, figure_2b, figure_2c, figure_3_1,
figure_3_2, figure_3_3, figure_3_4, figure_3_5, figure_3_6
> view figure_3_2
> view figure_3_3
> view figure_3_3
> view figure_3_4
> view figure_3_5
> view figure_3_5
> select #9/E:13-26,51-60
424 atoms, 425 bonds, 24 residues, 1 model selected
> color sel #ff85ffff
> color sel #ff8ad8ff
> color sel #d783ffff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name figure3_c
> view name figure3_C_2
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view list
Named views: figure3_C_2, figure3_c, figure_1, figure_2a, figure_2b,
figure_2c, figure_3_1, figure_3_2, figure_3_3, figure_3_4, figure_3_5,
figure_3_6
> view figure3_C_2
> select #9/E:51-60
171 atoms, 171 bonds, 10 residues, 1 model selected
> color sel #531b93ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3_C_zoomout.png" width
> 1704 height 1146 supersample 4 transparentBackground true
> select #9/G,B
2572 atoms, 2682 bonds, 118 residues, 1 model selected
> color sel #c0c0c0ff
> color sel #d6d6d6ff
> color sel #c0c0c0ff
> select #9/A,C,D,H
36930 atoms, 37350 bonds, 2444 residues, 1 model selected
> color sel #a9a9a9ff
> color sel #c0c0c0ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #fffb00ff
> select #9/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #8efa00ff
> select clear
> view figure3_C_2
> view figure_3_1
> select #9/B,C,D,E,G,H
23784 atoms, 24150 bonds, 1592 residues, 1 model selected
> hide sel cartoons
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #d6d6d6ff
> color sel #ebebebff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A.png" width 1704
> height 1146 supersample 4 transparentBackground true
> select #9/A
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #a9a9a9ff
> select #9/A:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #fffb00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_3.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #9 models
> show #10 models
> select #10/B,A,D,E,G,H
23784 atoms, 24150 bonds, 1592 residues, 1 model selected
> hide sel cartoons
> select #10/C
17067 atoms, 17243 bonds, 1050 residues, 1 model selected
> color sel #797979ff
> select #10/C:389-400
167 atoms, 169 bonds, 12 residues, 1 model selected
> color sel #8efa00ff
> select clear
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_4.png" width 1704
> height 1146 supersample 4 transparentBackground true
> show #9 models
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_5.png" width 1704
> height 1146 supersample 4 transparentBackground true
> hide #9 models
> hide #10 models
> show #!7 models
> hide #!7 surfaces
> save "/Users/amberms/Desktop/NEC Paper/figures/Figure3A_2.png" width 1704
> height 1146 supersample 4 transparentBackground true
> view name loopcloseup
> save "/Users/amberms/Desktop/NEC Paper/figures/012023.cxs"
——— End of log from Fri Jan 20 15:36:51 2023 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 430.140.3.0.0
OS Loader Version: 540.120.3~19
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 5 days 47 minutes
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2416D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: TN5PP6CO174S
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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