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Opened 3 weeks ago
Closed 3 weeks ago
#19136 closed defect (nonchimerax)
Crash in swap_buffers
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505160006 (2025-05-16 00:06:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Current thread 0x00007d00 (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 248 in swap_buffers
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 561 in swap_buffers
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\graphics\view.py", line 202 in draw
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\core\updateloop.py", line 84 in draw_new_frame
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\core\updateloop.py", line 150 in _redraw_timer_callback
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505160006\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages
---
warning | Registration file 'C:\\\Users\\\wailt\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has expired
UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 4UC1 fromDatabase pdb format mmcif
4uc1 title:
High resolution crystal structure of translocator protein 18kDa (TSPO) from
Rhodobacter sphaeroides (A139T Mutant) in C2 space group [more info...]
Chain information for 4uc1 #1
---
Chain | Description | UniProt
A B C | Translocator protein TspO | Q9RFC8_RHOSH 1-157
Non-standard residues in 4uc1 #1
---
MOE — methoxy-ethoxyl
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
P4C — O-acetaldehydyl-hexaethylene glycol (polyethylene 400)
PP9 — protoporphyrin IX
Z0P — (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
4uc1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 4UC3 fromDatabase pdb format mmcif
Summary of feedback from opening 4UC3 fetched from pdb
---
notes | Fetching compressed mmCIF 4uc3 from http://files.rcsb.org/download/4uc3.cif
Fetching CCD YZY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/YZY/YZY.cif
4uc3 title:
Translocator protein 18 kDa (TSPO) from Rhodobacter sphaeroides wild type
[more info...]
Chain information for 4uc3 #2
---
Chain | Description | UniProt
A B | TRANSLOCATOR PROTEIN TSPO | Q9RFC8_RHOSH 3-157
Non-standard residues in 4uc3 #2
---
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
YZY — (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
> select #1/A
1486 atoms, 1499 bonds, 198 residues, 1 model selected
> select #1/B
1461 atoms, 1480 bonds, 186 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/C
1348 atoms, 1361 bonds, 182 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/A
1486 atoms, 1499 bonds, 198 residues, 1 model selected
> hide sel atoms
> select clear
> select #2/B
1060 atoms, 1092 bonds, 1 pseudobond, 137 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #2/A
1216 atoms, 1247 bonds, 1 pseudobond, 152 residues, 2 models selected
> hide sel atoms
> select ::name="PP9"
42 atoms, 46 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui tool show Matchmaker
> matchmaker #!2 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 4uc1, chain A (#1) with 4uc3, chain A (#2), sequence alignment
score = 816.9
RMSD between 119 pruned atom pairs is 0.711 angstroms; (across all 143 pairs:
2.399)
> select add #1
4295 atoms, 4340 bonds, 566 residues, 1 model selected
> rainbow sel
> select clear
> color #2 #55007fff
> color #2 #00aaffff
> color #2 springgreen
> color #2 blue
> set bgColor white
> set bgColor #ffffff00
> color #2 #ffaa00ff
> color #2 #55ff7fff
> color #2 #00aa7fff
> color #2 #aa5500ff
> color #2 red
> hide #1 models
> hide #!2 models
> show #!2 models
> show #1 models
> select add #1
4295 atoms, 4340 bonds, 566 residues, 1 model selected
> color #2 #aaff00ff
> color #2 #00aa00ff
> color #2 lime
> hide #!2 models
> color #2 #aa00ffff
> show #!2 models
> color #2 #55007fff
> select clear
> lighting shadows true
> lighting full
> select ::name="PP9"
42 atoms, 46 bonds, 1 residue, 1 model selected
> style sel ball
Changed 42 atom styles
> ui tool show "Color Actions"
> color sel cyan target a
> color sel byhetero target a
> color sel forest green target a
> color sel cyan target a
> color sel light sea green target a
> color sel blue target a
> color sel cyan target a
> color sel byhetero target a
> select clear
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/RsTSPO_4UC1_4UC3_ChA.png
> width 1321 height 785 supersample 4 transparentBackground true
> select #1/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/RsTSPO_4UC1_4UC3_ChA2.png
> width 1321 height 785 supersample 4 transparentBackground true
> color #1 #d2724cff
> color #1 #59d261ff
> color #1 #1bd249ff
> color #1 #29d21dff
> color #2 #ff007fff
> lighting full
> graphics silhouettes true
> select clear
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/RsTSPO_4UC1_4UC3_ChA.png
> width 1321 height 785 supersample 4 transparentBackground true
> hide #!2.1 models
> select #1/A:33
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:33
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #1/A:34
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #1/A:31
36 atoms, 33 bonds, 4 residues, 1 model selected
> select add #1/A:30
50 atoms, 48 bonds, 5 residues, 1 model selected
> select add #1/A:29
59 atoms, 56 bonds, 6 residues, 1 model selected
> select subtract #1/A:31
47 atoms, 44 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1/A:31
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:31
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #1/A:138
25 atoms, 23 bonds, 3 residues, 1 model selected
> select subtract #1/A:138
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #1/A:35
28 atoms, 26 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select clear
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/RsTSPO_4UC1_4UC3_ChA2.png
> width 1321 height 785 supersample 4 transparentBackground true
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/RsTSPO_4UC1_4UC3_ChA.cxs
> close session
> open 2mgy fromDatabase pdb format mmcif
2mgy title:
Solution structure of the mitochondrial translocator protein (TSPO) in complex
with its high-affinity ligand PK11195 [more info...]
Chain information for 2mgy
---
Chain | Description | UniProt
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Translocator protein | Q99M32_MOUSE 1-169
> open 2N02 fromDatabase pdb format mmcif
Summary of feedback from opening 2N02 fetched from pdb
---
note | Fetching compressed mmCIF 2n02 from http://files.rcsb.org/download/2n02.cif
2n02 title:
Solution structure of the A147T variant of the mitochondrial translocator
protein (tspo) in complex with pk11195 [more info...]
Chain information for 2n02
---
Chain | Description | UniProt
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | Translocator protein | Q99M32_MOUSE 1-169
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.6 models
> hide #1.5 models
> hide #1.7 models
> hide #1.8 models
> hide #1.9 models
> hide #1.10 models
> hide #1.11 models
> hide #1.12 models
> hide #1.13 models
> show #1.13 models
> hide #1.13 models
> hide #1.14 models
> hide #1.15 models
> hide #1.16 models
> hide #1.17 models
> hide #1.18 models
> hide #1.19 models
> hide #1.20 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #2.9 models
> hide #2.10 models
> hide #2.11 models
> hide #2.12 models
> hide #2.13 models
> hide #2.14 models
> hide #2.15 models
> hide #2.16 models
> hide #2.17 models
> hide #2.18 models
> hide #2.19 models
> hide #2.20 models
> show #2.1 models
> ui tool show Matchmaker
> matchmaker #2.1 to #1.1
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 2mgy, chain A (#1.1) with 2n02, chain A (#2.1), sequence alignment
score = 855.7
RMSD between 115 pruned atom pairs is 1.143 angstroms; (across all 169 pairs:
4.576)
> hide #1.1#2.1 atoms
> select ::name="PKA"
1840 atoms, 1920 bonds, 40 residues, 40 models selected
> style sel & #1.1#2.1 stick
Changed 92 atom styles
> show sel & #1.1#2.1 atoms
> select clear
> color #2 #55ff00ff models
> color #1 #ff5500ff models
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/mTSPO_2mgy_2n02_ChA.cxs
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/mTSPO_2mgy_2n02_ChA.png
> width 1321 height 785 supersample 4 transparentBackground true
> save
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/mTSPO_2mgy_2n02_ChA2.png
> width 1321 height 785 supersample 4 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> close session
> open J:\PhD_Job\thesis_m\introduction\Presentation\all_strcutre.cxs format
> session
> set bgColor transparent
> view name session-start
opened ChimeraX session
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> hide #3.8 models
> hide #3.9 models
> hide #3.10 models
> hide #3.11 models
> hide #3.13 models
> hide #3.12 models
> hide #3.14 models
> hide #3.15 models
> hide #3.16 models
> hide #3.17 models
> hide #3.18 models
> hide #3.19 models
> hide #3.20 models
> show #3.1 models
> ui tool show Matchmaker
> matchmaker #2 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 4ryi, chain B (#1) with 4uc1, chain B (#2), sequence alignment
score = 312.8
RMSD between 118 pruned atom pairs is 1.026 angstroms; (across all 148 pairs:
1.896)
> matchmaker #3.1 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 4ryi, chain A (#1) with 2mgy, chain A (#3.1), sequence alignment
score = 274.8
RMSD between 31 pruned atom pairs is 1.056 angstroms; (across all 151 pairs:
6.501)
> matchmaker #!4 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 4ryi, chain B (#1) with 8e7w, chain B (#4), sequence alignment
score = 309.2
RMSD between 119 pruned atom pairs is 1.015 angstroms; (across all 148 pairs:
1.878)
> matchmaker #!5 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 4ryi, chain B (#1) with 8vgu, chain A (#5), sequence alignment
score = 940.5
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 151 pairs:
0.678)
> select #1/B
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> select #2/B
1461 atoms, 1480 bonds, 186 residues, 1 model selected
> select #2/C
1348 atoms, 1361 bonds, 182 residues, 1 model selected
> hide sel cartoons
> select #5/B
1364 atoms, 1382 bonds, 6 pseudobonds, 183 residues, 2 models selected
> hide sel cartoons
> select #4/C
1262 atoms, 1278 bonds, 179 residues, 1 model selected
> select #1/B
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> select #1/B
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> select #1/A
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> select clear
> select #1/B
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> hide sel cartoons
> matchmaker #2#3.1#!4-5 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 4ryi, chain B (#1) with 4uc1, chain B (#2), sequence alignment
score = 312.8
RMSD between 118 pruned atom pairs is 1.026 angstroms; (across all 148 pairs:
1.896)
Matchmaker 4ryi, chain A (#1) with 2mgy, chain A (#3.1), sequence alignment
score = 274.8
RMSD between 31 pruned atom pairs is 1.056 angstroms; (across all 151 pairs:
6.501)
Matchmaker 4ryi, chain B (#1) with 8e7w, chain B (#4), sequence alignment
score = 309.2
RMSD between 119 pruned atom pairs is 1.015 angstroms; (across all 148 pairs:
1.878)
Matchmaker 4ryi, chain B (#1) with 8vgu, chain A (#5), sequence alignment
score = 940.5
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 151 pairs:
0.678)
> matchmaker #2#3.1#!4-5 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 4ryi, chain B (#1) with 4uc1, chain B (#2), sequence alignment
score = 312.8
RMSD between 118 pruned atom pairs is 1.026 angstroms; (across all 148 pairs:
1.896)
Matchmaker 4ryi, chain A (#1) with 2mgy, chain A (#3.1), sequence alignment
score = 274.8
RMSD between 31 pruned atom pairs is 1.056 angstroms; (across all 151 pairs:
6.501)
Matchmaker 4ryi, chain B (#1) with 8e7w, chain B (#4), sequence alignment
score = 309.2
RMSD between 119 pruned atom pairs is 1.015 angstroms; (across all 148 pairs:
1.878)
Matchmaker 4ryi, chain B (#1) with 8vgu, chain A (#5), sequence alignment
score = 940.5
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 151 pairs:
0.678)
> matchmaker #2 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 4ryi, chain B (#1) with 4uc1, chain B (#2), sequence alignment
score = 312.8
RMSD between 118 pruned atom pairs is 1.026 angstroms; (across all 148 pairs:
1.896)
No reference and/or match structure/chain chosen
> matchmaker #2 & sel to #1
No molecules/chains to match specified
> close #3.19
> close
> open "Y:/alignement tspo/alignement bctspo/Bc TSPO/Bc TSPO
> chaine/4ryichA.pdb"
Chain information for 4ryichA.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> close
> open "Y:/alignement tspo/alignement bctspo/Bc TSPO/Bc TSPO chaine/4ryichA-
> PK.pdb"
Chain information for 4ryichA-PK.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "Y:/alignement tspo/alignement bctspo/Rs TSPO/Rs TSPO
> cha/4uc1chApp9.pdb"
Chain information for 4uc1chApp9.pdb #2
---
Chain | Description
A | No description available
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> open C:/Users/wailt/Downloads/ChimeraX/PDB/2mgy.cif
2mgy.cif title:
Solution structure of the mitochondrial translocator protein (TSPO) in complex
with its high-affinity ligand PK11195 [more info...]
Chain information for 2mgy.cif
---
Chain | Description | UniProt
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A | Translocator protein | Q99M32_MOUSE 1-169
> select add #3
53820 atoms, 54940 bonds, 3400 residues, 21 models selected
> close
> open C:/Users/wailt/Downloads/ChimeraX/PDB/4ryi.cif
4ryi.cif title:
Crystal structure of BcTSPO/PK11195 complex [more info...]
Chain information for 4ryi.cif #1
---
Chain | Description | UniProt
A B | Integral membrane protein | Q81BL7_BACCR 1-153
Non-standard residues in 4ryi.cif #1
---
PKA —
N-[(2R)-butan-2-yl]-1-(2-chlorophenyl)-N-methylisoquinoline-3-carboxamide
4ryi.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select /B
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> open 4UC1 fromDatabase pdb format mmcif
4uc1 title:
High resolution crystal structure of translocator protein 18kDa (TSPO) from
Rhodobacter sphaeroides (A139T Mutant) in C2 space group [more info...]
Chain information for 4uc1 #2
---
Chain | Description | UniProt
A B C | Translocator protein TspO | Q9RFC8_RHOSH 1-157
Non-standard residues in 4uc1 #2
---
MOE — methoxy-ethoxyl
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
P4C — O-acetaldehydyl-hexaethylene glycol (polyethylene 400)
PP9 — protoporphyrin IX
Z0P — (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate
4uc1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #2
5569 atoms, 5662 bonds, 718 residues, 2 models selected
> select subtract #2
1274 atoms, 1322 bonds, 152 residues, 1 model selected
> select add #1
2548 atoms, 2644 bonds, 304 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
4295 atoms, 4340 bonds, 566 residues, 1 model selected
> hide sel atoms
> select #2/B
1461 atoms, 1480 bonds, 186 residues, 1 model selected
> hide sel cartoons
> select #2/B
1461 atoms, 1480 bonds, 186 residues, 1 model selected
> select add #1
4009 atoms, 4124 bonds, 490 residues, 2 models selected
> select clear
> select #2/C
1348 atoms, 1361 bonds, 182 residues, 1 model selected
> hide sel cartoons
> select #2/A
1486 atoms, 1499 bonds, 198 residues, 1 model selected
> select clear
> open J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/2mgy.pdb
Chain information for 2mgy.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> close
> open J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/2mgy.pdb
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/4RYI.pdb
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/4UC1.pdb
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/8e7w.pdb
> J:/PhD_Job/thesis_m/introduction/Pic_created/3D_strcutres/8vgu.pdb
Chain information for 2mgy.pdb #1
---
Chain | Description
A | No description available
Chain information for 4RYI.pdb #2
---
Chain | Description
A | No description available
Chain information for 4UC1.pdb #3
---
Chain | Description
A | No description available
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 8e7w.pdb #4
---
Chain | Description
B | No description available
Chain information for 8vgu.pdb #5
---
Chain | Description
A | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #3#!4-5 to #2
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 4RYI.pdb, chain A (#2) with 4UC1.pdb, chain A (#3), sequence
alignment score = 303.6
RMSD between 114 pruned atom pairs is 1.081 angstroms; (across all 148 pairs:
2.048)
Matchmaker 4RYI.pdb, chain A (#2) with 8e7w.pdb, chain B (#4), sequence
alignment score = 304.2
RMSD between 117 pruned atom pairs is 1.046 angstroms; (across all 148 pairs:
1.900)
Matchmaker 4RYI.pdb, chain A (#2) with 8vgu.pdb, chain A (#5), sequence
alignment score = 803.2
RMSD between 151 pruned atom pairs is 0.610 angstroms; (across all 151 pairs:
0.610)
> matchmaker #1 to #2
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 4RYI.pdb, chain A (#2) with 2mgy.pdb, chain A (#1), sequence
alignment score = 276.9
RMSD between 31 pruned atom pairs is 1.056 angstroms; (across all 151 pairs:
6.401)
> hide atoms
> hide #1 models
> hide #3 models
> hide #!4 models
> select ::name="PKA"
71 atoms, 75 bonds, 2 residues, 2 models selected
> show sel & #2 atoms
> select ::name="MH0"
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> show sel atoms
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file 'C:\\\Users\\\wailt\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has expired
UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 - Build 20.19.15.4835
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel
Python: 3.11.4
Locale: fr_FR.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Microsoft Windows 11 Professionnel (Build 26100)
Memory: 17,079,345,152
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
OSLanguage: fr-FR
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.3
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.6
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505160006
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
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: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
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-StarMap: 1.2.15
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
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-TugLigands: 1.1
ChimeraX-UI: 1.45.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.1.0
narwhals: 1.44.0
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: 2.2.6
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.1
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pyqtgraph: 0.13.7
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.2
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.2
tornado: 6.5
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Change History (2)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers |
comment:2 by , 3 weeks ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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Graphics driver crash, Windows, Intel(R) HD Graphics 4600, driver 20.19.15.4835 circa 2017.