Opened 3 years ago

Closed 3 years ago

#7697 closed defect (can't reproduce)

Crash during window resize in QOpenGLContext.makeCurrent()

Reported by: chimerax-bug-report@… 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-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 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 0x00001934 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 111 in make_current
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 490 in make_current
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 104 in _use_opengl
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 139 in draw
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 73 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 158 in update_graphics_now
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\graphics.py", line 145 in resizeEvent
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\graphics.py", line 57 in event
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open "D:/MicroBiology/卒業研究/ROA2 kw(laccase)/'22.9.4 Locus_08480.pdb"

Chain information for '22.9.4 Locus_08480.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.4 Locus_08480.pdb, chain (blank) (#2), sequence alignment score = 77.9  
RMSD between 6 pruned atom pairs is 1.280 angstroms; (across all 168 pairs:
19.660)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_02230.pdb"

Chain information for '22.9.6 Locus_02230.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_02230.pdb, chain (blank) (#2), sequence alignment score = 190.9  
RMSD between 101 pruned atom pairs is 0.951 angstroms; (across all 216 pairs:
7.361)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/?

Alignment identifier is 2/  

> hide #1 models

> select #2/*:146

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/*:146

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #1 models

> hide #1 models

> select #2/*:237

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:237

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/*:269

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/*:269

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #1 models

> select #2/*:148

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/*:148-151

27 atoms, 27 bonds, 4 residues, 1 model selected  

> hide #1 models

> select ::name="CYS"

24 atoms, 22 bonds, 4 residues, 1 model selected  

> show #1 models

> select clear

> hide #2 models

> show #2 models

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_09810.pdb"

Chain information for '22.9.6 Locus_09810.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_09810.pdb, chain (blank) (#2), sequence alignment score = 53.6  
RMSD between 5 pruned atom pairs is 0.937 angstroms; (across all 121 pairs:
16.155)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_11230.pdb"

Chain information for '22.9.6 Locus_11230.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_11230.pdb, chain (blank) (#2), sequence alignment score = 95.3  
RMSD between 9 pruned atom pairs is 1.498 angstroms; (across all 178 pairs:
20.821)  
  

> hide #1 models

> close #2

> show #1 models

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_11230_intensive.pdb"

Chain information for Locus_11230_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_11230_intensive.pdb, chain (blank) (#2), sequence alignment score = 78.2  
RMSD between 12 pruned atom pairs is 1.006 angstroms; (across all 228 pairs:
24.370)  
  

> hide #1 models

> close #2

> show #1 models

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_13310.pdb"

Chain information for '22.9.6 Locus_13310.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_13310.pdb, chain (blank) (#2), sequence alignment score = 47.8  
RMSD between 5 pruned atom pairs is 1.003 angstroms; (across all 198 pairs:
20.970)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_13310_intensive.pdb"

Chain information for Locus_13310_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_13310_intensive.pdb, chain (blank) (#2), sequence alignment score = 46.6  
RMSD between 17 pruned atom pairs is 0.660 angstroms; (across all 117 pairs:
26.952)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_13770.pdb"

Chain information for '22.9.6 Locus_13770.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_13770.pdb, chain (blank) (#2), sequence alignment score = 146.1  
RMSD between 38 pruned atom pairs is 1.024 angstroms; (across all 221 pairs:
15.974)  
  

> hide #1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/?

Alignment identifier is 2/  

> select #2/*:171-172

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #2/*:171-172

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #2/*:171-172

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #2/*:170-171

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #2/*:171

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/*:171

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/*:299

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/*:299

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/*:273-274

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #2/*:273-274

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #2/*:273

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:273

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:270

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:261-270

70 atoms, 71 bonds, 10 residues, 1 model selected  

> select #2/*:263-264

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #2/*:263-270

55 atoms, 56 bonds, 8 residues, 1 model selected  

> select #2/*:265

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/*:265-273

67 atoms, 68 bonds, 9 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #2/*:271

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:271

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #1 models

> select #2/*:173

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/*:173-176

21 atoms, 20 bonds, 4 residues, 1 model selected  

> hide #1 models

> select ::name="CYS"

42 atoms, 37 bonds, 7 residues, 2 models selected  

> close #2

> show #1 models

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_14590.pdb"

Chain information for '22.9.6 Locus_14590.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_14590.pdb, chain (blank) (#2), sequence alignment score = 61.8  
RMSD between 15 pruned atom pairs is 1.044 angstroms; (across all 178 pairs:
19.917)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_14590_intensive.pdb"

Chain information for Locus_14590_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_14590_intensive.pdb, chain (blank) (#2), sequence alignment score = 35.7  
RMSD between 5 pruned atom pairs is 1.208 angstroms; (across all 76 pairs:
40.339)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_18010.pdb"

Chain information for '22.9.6 Locus_18010.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_18010.pdb, chain (blank) (#2), sequence alignment score = 21.1  
RMSD between 17 pruned atom pairs is 0.675 angstroms; (across all 56 pairs:
25.004)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_18010_intensive.pdb"

Chain information for Locus_18010_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_18010_intensive.pdb, chain (blank) (#2), sequence alignment score = 25  
RMSD between 4 pruned atom pairs is 1.277 angstroms; (across all 155 pairs:
37.137)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_18030.pdb"

Chain information for '22.9.6 Locus_18030.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_18030.pdb, chain (blank) (#2), sequence alignment score = 45.9  
RMSD between 8 pruned atom pairs is 1.202 angstroms; (across all 146 pairs:
18.244)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_19020.pdb"

Chain information for '22.9.6 Locus_19020.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_19020.pdb, chain (blank) (#2), sequence alignment score = 88.4  
RMSD between 80 pruned atom pairs is 1.034 angstroms; (across all 209 pairs:
14.084)  
  

> hide #1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/?

Alignment identifier is 2/  

> select #2/*:139

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/*:139

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/*:263

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:263

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/*:291

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/*:291

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #1 models

> hide #1 models

> select ::name="CYS"

30 atoms, 27 bonds, 5 residues, 2 models selected  

> close #2

> show #1 models

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_22870.pdb"

Chain information for '22.9.6 Locus_22870.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_22870.pdb, chain (blank) (#2), sequence alignment score = 70.9  
RMSD between 6 pruned atom pairs is 1.467 angstroms; (across all 193 pairs:
24.496)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_22870_intensive.pdb"

Chain information for Locus_22870_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_22870_intensive.pdb, chain (blank) (#2), sequence alignment score = 63.6  
RMSD between 9 pruned atom pairs is 0.694 angstroms; (across all 206 pairs:
23.671)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_25800.pdb"

Chain information for '22.9.6 Locus_25800.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_25800.pdb, chain (blank) (#2), sequence alignment score = 28.2  
RMSD between 7 pruned atom pairs is 1.632 angstroms; (across all 30 pairs:
9.786)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_26170.pdb"

Chain information for '22.9.6 Locus_26170.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_26170.pdb, chain (blank) (#2), sequence alignment score = 54.4  
RMSD between 12 pruned atom pairs is 0.800 angstroms; (across all 181 pairs:
21.152)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_26170_intensive.pdb"

Chain information for Locus_26170_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_26170_intensive.pdb, chain (blank) (#2), sequence alignment score = 66.9  
RMSD between 6 pruned atom pairs is 1.347 angstroms; (across all 153 pairs:
22.406)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_27130.pdb"

Chain information for '22.9.6 Locus_27130.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_27130.pdb, chain (blank) (#2), sequence alignment score = 84.4  
RMSD between 5 pruned atom pairs is 1.324 angstroms; (across all 160 pairs:
26.398)  
  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for '22.9.4 Ideonella_sakaiensis PETase.pdb_ SES surface
#1.1: minimum, -15.23, mean 0.86, maximum 12.85  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select #1/?#2/?

4947 atoms, 5056 bonds, 650 residues, 2 models selected  

> mlp sel

Map values for surface "'22.9.6 Locus_27130.pdb_ SES surface": minimum -28.4,
mean -4.128, maximum 27.46  
Map values for surface "'22.9.4 Ideonella_sakaiensis PETase.pdb_ SES surface":
minimum -30.66, mean -7.145, maximum 22.84  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide sel & #!1 surfaces

> show sel & #!1 surfaces

> hide sel & #!1 surfaces

> show sel & #!1 surfaces

> coulombic sel & #!1

Coulombic values for '22.9.4 Ideonella_sakaiensis PETase.pdb_ SES surface
#1.1: minimum, -15.23, mean 0.86, maximum 12.85  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel & #!1 surfaces

> ~select #1

3012 atoms, 3074 bonds, 387 residues, 3 models selected  

> ~select #2

1 model selected  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_27130_intensive.pdb"

Chain information for Locus_27130_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_27130_intensive.pdb, chain (blank) (#2), sequence alignment score = 82.8  
RMSD between 20 pruned atom pairs is 1.116 angstroms; (across all 191 pairs:
19.897)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_30240.pdb"

Chain information for '22.9.6 Locus_30240.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_30240.pdb, chain (blank) (#2), sequence alignment score = 34.5  
RMSD between 3 pruned atom pairs is 1.209 angstroms; (across all 77 pairs:
21.598)  
  

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result
> (lipase)/Locus_30240_intensive.pdb"

Chain information for Locus_30240_intensive.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
Locus_30240_intensive.pdb, chain (blank) (#2), sequence alignment score = 27.7  
RMSD between 4 pruned atom pairs is 1.260 angstroms; (across all 78 pairs:
22.028)  
  

> hide #!1 models

> select #2

2805 atoms, 2889 bonds, 343 residues, 1 model selected  

> mlp sel

Map values for surface "Locus_30240_intensive.pdb_ SES surface": minimum
-26.98, mean -2.624, maximum 23.55  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> hide #!2 models

> show #!1 models

> close #2

> open "D:/MicroBiology/卒業研究/ROA2 kw(lipase)/Phyre2 result (lipase)/'22.9.6
> Locus_30340.pdb"

Chain information for '22.9.6 Locus_30340.pdb #2  
---  
Chain | Description  
? | No description available  
  

> 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 '22.9.4 Ideonella_sakaiensis PETase.pdb, chain (blank) (#1) with
'22.9.6 Locus_30340.pdb, chain (blank) (#2), sequence alignment score = 146.8  
RMSD between 47 pruned atom pairs is 1.030 angstroms; (across all 220 pairs:
12.805)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/?

Alignment identifier is 2/  

> hide #!1 models

> select #2/*:158

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/*:158

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/*:280

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/*:280

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!1 models

> hide #!1 models

> select #2/*:249

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/*:249

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Pro 6
OS: Microsoft Windows 11 Pro (Build 22000)
Memory: 8,502,890,496
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8350U CPU @ 1.70GHz
OSLanguage: ja-JP
Locale: ('ja_JP', 'cp932')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash during window resize

comment:2 by Tom Goddard, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash during window resize → Crash during window resize in QOpenGLContext.makeCurrent()

Crashed making opengl context current. Could be a Qt bug, could be an OpenGL driver crash, could be the resize event is called in a non-gui thread.

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