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#9837 closed defect (can't reproduce)

Crashed in Qt event loop after opening a session

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-10-10.0.19044
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: code 0x80000003

Current thread 0x00000678 (most recent call first):
  File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> close #2

> close #6

> close #7

> open "E:/sui lab/CC/MCC_science_report/new
> pdbs/map/J318_002_volume_map_pc.mrc"

Opened J318_002_volume_map_pc.mrc as #2, grid size 320,320,320, pixel 1.1,
shown at level 0.139, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.1233

> ui tool show "Hide Dust"

> surface dust #2 size 11.87

> surface dust #2 size 10.47

> volume #2 level 0.1032

> volume #2 level 0.1092

> volume #2 level 0.12

> volume #2 level 0.115

> show #4 models

> hide #4 models

> show #4 models

> hide #!2 models

> color #4 bychain

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #4 distance 6.59

> volume splitbyzone #2

Opened J318_002_volume_map_pc.mrc 0 as #6.1, grid size 320,320,320, pixel 1.1,
shown at level 0.115, step 1, values float32  
Opened J318_002_volume_map_pc.mrc 1 as #6.2, grid size 320,320,320, pixel 1.1,
shown at level 0.115, step 1, values float32  
Opened J318_002_volume_map_pc.mrc 2 as #6.3, grid size 320,320,320, pixel 1.1,
shown at level 0.115, step 1, values float32  
Opened J318_002_volume_map_pc.mrc 3 as #6.4, grid size 320,320,320, pixel 1.1,
shown at level 0.115, step 1, values float32  
Opened J318_002_volume_map_pc.mrc 4 as #6.5, grid size 320,320,320, pixel 1.1,
shown at level 0.115, step 1, values float32  

> hide #!6.1 models

> show #!3 models

> hide #!6.2 models

> hide #!6.3 models

> hide #!6.5 models

> select #3

21080 atoms, 21564 bonds, 2740 residues, 1 model selected  

> transparency sel 0 target c

> ~select #3

4 models selected  

> surface dust #6.5 size 9.98

> surface dust #6.5 size 13.93

> surface dust #6.4 size 9.51

> hide #4 models

> select #3/B,C,D

15810 atoms, 16173 bonds, 2055 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #4 models

> select #3/B,A,D

15810 atoms, 16173 bonds, 2055 residues, 1 model selected  

> select #4/B,A,D

15768 atoms, 16122 bonds, 2052 residues, 1 model selected  

> hide sel cartoons

> color #6.4 white models transparency 0

> color #6.4 #d6d6d6 models transparency 0

> color #6.4 #d9d9d9 models transparency 0

> transparency #3.1-4#6.4.1 0

> select #6.4

2 models selected  

> transparency sel 50

> ~select #6.4

Nothing selected  

> color #4 #aa00ff transparency 0

> cartoon style #3-4#6.4#!6 modeHelix tube sides 20

> volume #2 level 0.11

> volume #6.4 level 0.11

> color #6.4 #cbcbcb80 models

> color #6.4 #e6e6e680 models

> color #6.4 #dadada80 models

> volume #6.4 level 0.12

> volume #6.4 level 0.115

> volume #6.4 level 0.11

> select #4/C:1095-1178

631 atoms, 639 bonds, 84 residues, 1 model selected  

> color sel lime

> color sel blue

> color sel hot pink

> select clear

> select #4/C:1095-1178

631 atoms, 639 bonds, 84 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel yellow

> select clear

> select #4/C:1095

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

> color sel purple

> color sel magenta

> select clear

> select #4/C:1095

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

> color sel purple

> select clear

> select #4/C:1095

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

> ui tool show "Color Actions"

> color sel magenta

> select clear

> color #4 #b16cff transparency 0

> color #4 #aa00ff transparency 0

> color #4 #aa007f transparency 0

> color #4 #aa55ff transparency 0

> color #4 #aa00ff transparency 0

> color #4 #ff55ff transparency 0

> color #4 magenta transparency 0

> select #4

21024 atoms, 21496 bonds, 2736 residues, 1 model selected  

> color sel magenta

> select clear

> select #4

21024 atoms, 21496 bonds, 2736 residues, 1 model selected  

> color sel hot pink

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel yellow

> select clear

> save "E:/sui lab/CC/MCC_science_report/20230921-new/PC1.jpg" width 1288
> height 788 supersample 3

> select #4/C:1105-1178

545 atoms, 549 bonds, 74 residues, 1 model selected  

> color sel yellow

> color sel hot pink

> select clear

> save "E:/sui lab/CC/MCC_science_report/20230921-new/PC2.jpg" width 1288
> height 788 supersample 3

> select #4/C:1096-1104

78 atoms, 81 bonds, 9 residues, 1 model selected  

> color sel forest green

> color sel medium blue

> color sel red

> select clear

> select #4/C:1096-1104

78 atoms, 81 bonds, 9 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel orange

> color sel dark orange

> select clear

> select #4/C:1096-1104

78 atoms, 81 bonds, 9 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel sea green

> color sel medium blue

> color sel indigo

> color sel brown

> color sel olive drab

> color sel sea green

> color sel forest green

> select clear

> select #4/C:1096-1104

78 atoms, 81 bonds, 9 residues, 1 model selected  

> select clear

> select #4/C:1096-1104

78 atoms, 81 bonds, 9 residues, 1 model selected  

> color sel medium blue

> select clear

> save "E:/sui lab/CC/MCC_science_report/20230921-new/3.jpg" width 1288 height
> 785 supersample 3

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> select clear

> save "E:/sui lab/CC/MCC_science_report/20230921-new/4.jpg" width 1288 height
> 785 supersample 3

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark blue

> select clear

> save "E:/sui lab/CC/MCC_science_report/20230921-new/5.jpg" width 1288 height
> 785 supersample 3

> save "E:/sui lab/CC/MCC_science_report/20230921-new/6.jpg" width 1288 height
> 785 supersample 3

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel red

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel orange

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel lime

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel medium blue

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel black

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> color sel gray

> select clear

> select #4/C:1096-1178

623 atoms, 631 bonds, 83 residues, 1 model selected  

> ui tool show "Color Actions"

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1285,  
description = b'\xc4\xda\xb4\xe6\xb2\xbb\xd7\xe3',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1288,  
644,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1288,  
644,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1288,  
644,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
)  
)  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line
73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line
165, in draw  
self._draw_scene(camera, drawings)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line
214, in _draw_scene  
silhouette.start_silhouette_drawing(r)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line
1757, in start_silhouette_drawing  
fb = self._silhouette_framebuffer(r)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line
1793, in _silhouette_framebuffer  
dt.initialize_depth(size, depth_compare_mode=False)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line
2916, in initialize_depth  
self.initialize_texture(size, format, iformat, tdtype, ncomp,  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line
2942, in initialize_texture  
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'\xc4\xda\xb4\xe6\xb2\xbb\xd7\xe3',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1288,  
644,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1288,  
644,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1288,  
644,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
)  
)  
  
Exception ignored in:   
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line
3003, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  


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

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

> open "E:\\\sui lab\\\CC\\\MCC_science_report\\\20230921-new\\\fig\\\PC-
> whole.cxs"

Opened J380_006_volume_map_whole_pc.mrc as #7, grid size 320,320,320, pixel
1.1, shown at level 0.0398, step 1, values float32  
Log from Sat Sep 23 17:14:46 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "E:\\\sui lab\\\CC\\\MCC_science_report\\\new pdbs\\\pse and
> cxs\\\PCalign.cxs"

Log from Sun Nov 27 19:32:21 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "E:\\\sui lab\\\CC\\\MCC_science_report\\\new pdbs\\\pse and
> cxs\\\PCalign.cxs"

Log from Thu Nov 24 20:35:17 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/sui lab/CC/MCC_science_report/new pdbs/PC-final-lds.pdb"

Summary of feedback from opening E:/sui lab/CC/MCC_science_report/new pdbs/PC-
final-lds.pdb  
---  
warning | Ignored bad PDB record found on line 1  
  
Chain information for PC-final-lds.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open "E:/sui lab/CC/MCC_science_report/new pdbs/PC-state2-final.pdb"

Chain information for PC-state2-final.pdb #2  
---  
Chain | Description  
A B C D | 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 PC-final-lds.pdb, chain A (#1) with PC-state2-final.pdb, chain A
(#2), sequence alignment score = 3458  
RMSD between 676 pruned atom pairs is 0.105 angstroms; (across all 681 pairs:
0.341)  
  

> set bgColor white

> lighting soft

> color #1 #9ba5d2 transparency 0

> color #1 #d29bc8 transparency 0

> color #1 #d281ce transparency 0

> color #1 #cb78d2 transparency 0

> color #1 #c16cd2 transparency 0

> color #1 #a37bd2 transparency 0

> color #1 #d272c2 transparency 0

> color #1 #d26bc1 transparency 0

> color #1 #d267c0 transparency 0

> hide #1 models

> show #1 models

> color bychain

> color bypolymer

> color #1 #d589d1 transparency 0

> color #1 #cc89d5 transparency 0

> color #2 #85f2eb transparency 0

> color #2 #66f289 transparency 0

> color #2 #62f286 transparency 0

> color #2 #f2e3a6 transparency 0

> color #2 #cbf2b6 transparency 0

> color #2 #baf2aa transparency 0

> lighting flat

> lighting soft

> graphics silhouettes false

> lighting soft

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> open "E:/sui lab/CC/MCC_science_report/PC_new/molcell/7wta.pdb"

7wta.pdb title:  
Cryo-em structure of human pyruvate carboxylase In apo state [more info...]  
  
Chain information for 7wta.pdb #3  
---  
Chain | Description | UniProt  
A B C D | pyruvate carboxylase, mitochondrial | PYC_HUMAN  
  
Non-standard residues in 7wta.pdb #3  
---  
BTI — 5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal  
  

> ui tool show Matchmaker

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PC-final-lds.pdb, chain A (#1) with 7wta.pdb, chain B (#3),
sequence alignment score = 3227  
RMSD between 532 pruned atom pairs is 1.246 angstroms; (across all 684 pairs:
15.713)  
  

> color #3 #acd0dd transparency 0

> hide #!2 models

> color #1 #d568a2 transparency 0

> color #1 #d56bc7 transparency 0

> color #1 #bc70d5 transparency 0

> color #1 #cc4fd5 transparency 0

> color #1 #d14fd5 transparency 0

> select #1/A,D,C

15768 atoms, 16122 bonds, 2052 residues, 1 model selected  

> transparency sel 80 target c

> select #3

21080 atoms, 21564 bonds, 2740 residues, 1 model selected  

> ~select #3

Nothing selected  

> select clear

> select #2/A,D,B

24531 atoms, 25062 bonds, 3 pseudobonds, 3174 residues, 2 models selected  

> select #3/A,D,B

15810 atoms, 16173 bonds, 2055 residues, 1 model selected  

> transparency sel 80 target c

> select clear

> select #3/A,D,B

15810 atoms, 16173 bonds, 2055 residues, 1 model selected  

> transparency sel 90 target c

> select #1/A,D,C

15768 atoms, 16122 bonds, 2052 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> hide #1,3 atoms

> select ::name="BTI"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> style sel ball

Changed 60 atom styles  

> select clear

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> transparency sel 0 target c

> select clear

> hide #1,3 atoms

> select #3/A:BTI

15 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel red

> color sel byhetero

> select clear

> show #1,3 surfaces

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> color #!1,3 bychain

[Repeated 1 time(s)]

> hide #!1,3 surfaces

> color #1 #f068d0 transparency 0

> color #1 #f05fee transparency 0

> color #3 #91bcb5 transparency 0

> color #3 #6cbcb5 transparency 0

> color #3 #81e2da transparency 0

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> select #1/A,D,C

15768 atoms, 16122 bonds, 2052 residues, 1 model selected  

> transparency sel 90 target c

> select #3/A,D,B

15810 atoms, 16173 bonds, 2055 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> transparency sel 0 target c

> color (#!3 & sel) blue

> select clear

> select #1/B:1095-1178

631 atoms, 639 bonds, 84 residues, 1 model selected  

> color (#!1 & sel) red

> select clear

> cartoon style #1,3 modeHelix tube sides 20

> select down

Nothing selected  

> cartoon style #1,3 xsection rectangle modeHelix default

> graphics silhouettes false

> graphics silhouettes true

> select #1/A,D,C

15768 atoms, 16122 bonds, 2052 residues, 1 model selected  

> transparency sel 95 target c

> select clear

> select #1/A,D,C

15768 atoms, 16122 bonds, 2052 residues, 1 model selected  

> transparency sel 100 target c

> select clear

> graphics silhouettes false

> graphics silhouettes true

> color #1 #f058ed00

> color #1 #f05dee00

> color #1 #f060f000

> color #3 #74e2d219

> select #1/B

5256 atoms, 5374 bonds, 684 residues, 1 model selected  

> transparency sel 0 target c

> select clear

> select #3/C

5270 atoms, 5391 bonds, 685 residues, 1 model selected  

> transparency sel 0 target c

> select clear

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> transparency sel 0 target c

> select clear

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> color (#!3 & sel) blue

> select clear

> select #3/C:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> color (#!3 & sel) blue

> select clear

> color #1 #f0e6c400

> color #1 #f0d59800

> color #1 #f0e08f00

> color #1 #c4d0f000

> select #1/B

5256 atoms, 5374 bonds, 684 residues, 1 model selected  

> transparency sel 0 target c

> color (#!1 & sel) #ff061fff

> color (#!1 & sel) #ff0617ff

> color (#!1 & sel) #ff1121ff

> color (#!1 & sel) #ff1e3cff

> color (#!1 & sel) #ff2243ff

> color (#!1 & sel) #ff234bff

> color (#!1 & sel) #ff2566ff

> color (#!1 & sel) #ff2667ff

> color (#!1 & sel) #ff2365ff

> color (#!1 & sel) #ff2155ff

> color (#!1 & sel) #ff1d4eff

> color (#!1 & sel) #ff1d65ff

> color (#!1 & sel) #ff1d77ff

> color (#!1 & sel) #ff1dbbff

> color (#!1 & sel) #ff1ebcff

> color (#!1 & sel) #ff20bcff

> color (#!1 & sel) #ff20b8ff

> color (#!1 & sel) #ff25a1ff

> color (#!1 & sel) #ff3385ff

> color (#!1 & sel) #ff4183ff

> color (#!1 & sel) #ff497aff

> color (#!1 & sel) #ff4c64ff

> color (#!1 & sel) #ff4e5aff

> color (#!1 & sel) #ff4e57ff

> color (#!1 & sel) #ff4e51ff

> color (#!1 & sel) #ff4c4fff

> color (#!1 & sel) #ff4649ff

> color (#!1 & sel) #ff4346ff

> color (#!1 & sel) #ff4043ff

> color (#!1 & sel) #ff3e41ff

> color (#!1 & sel) #ff3d40ff

> color (#!1 & sel) #ff3c3fff

> color (#!1 & sel) #ff3a47ff

> color (#!1 & sel) #ff3877ff

> color (#!1 & sel) #ff389fff

> color (#!1 & sel) #ff38b3ff

> color (#!1 & sel) #ff38c3ff

> color (#!1 & sel) #ff38d1ff

> color (#!1 & sel) #ff39deff

> color (#!1 & sel) #ff45d7ff

> color (#!1 & sel) #ff59d3ff

> color (#!1 & sel) #ff66d6ff

> color (#!1 & sel) #ff6ad7ff

> color (#!1 & sel) #ff6bd8ff

> color (#!1 & sel) #ff6bd3ff

> color (#!1 & sel) #ff5ac5ff

> color (#!1 & sel) #ff52aeff

> color (#!1 & sel) #ff50a5ff

> color (#!1 & sel) #ff509fff

> color (#!1 & sel) #ff5096ff

> color (#!1 & sel) #ff5084ff

> color (#!1 & sel) #ff507fff

> color (#!1 & sel) #ff5070ff

> color (#!1 & sel) #ff5061ff

> color (#!1 & sel) #ff5059ff

> color (#!1 & sel) #ff505cff

> color (#!1 & sel) #ff5070ff

> color (#!1 & sel) #ff4f87ff

> color (#!1 & sel) #ff4e8cff

> color (#!1 & sel) #ff4c94ff

> color (#!1 & sel) #ff49b0ff

> color (#!1 & sel) #ff46beff

> color (#!1 & sel) #ff43c7ff

> color (#!1 & sel) #ff41ccff

> color (#!1 & sel) #ff41c6ff

> color (#!1 & sel) #ff41c3ff

> select #3/C:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> color (#!3 & sel) cyan

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> color (#!3 & sel) cyan

> select clear

> select #3/A:1095-1101

65 atoms, 67 bonds, 7 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #3/A:1095-1178

630 atoms, 638 bonds, 84 residues, 1 model selected  

> transparency sel 100 target c

> select clear

> select ::name="BTI"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 60 atom styles  

> color sel byhetero

> select clear

> show #!1,3 atoms

> hide #!1,3 atoms

> select ::name="BTI"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> style sel ball

Changed 60 atom styles  

> select #3/A:BTI

15 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 15 atom styles  

> color sel byhetero

> transparency sel 0 target c

[Repeated 1 time(s)]

> transparency sel 0 target a

> select #3/C:BTI

15 atoms, 16 bonds, 1 residue, 1 model selected  

> transparency sel 0 target a

> show sel atoms

> select clear

> undo

> transparency sel 80 target a

> transparency sel 50 target a

> select clear

> open "E:/sui lab/CC/MCC_science_report/new pdbs/PC-final-coot-1.pdb"

Chain information for PC-final-coot-1.pdb #4  
---  
Chain | Description  
A B C D | No description available  
  

> color #4 #ee78e4 transparency 0

> color #4 #ee8aee transparency 0

> hide #4 models

> save "E:/sui lab/CC/MCC_science_report/new pdbs/figure/pc.jpg" width 1336
> height 776 supersample 3

> show #!2 models

> close #2

> open "E:/sui lab/CC/MCC_science_report/PC_new/molcell/7wtc.pdb"

7wtc.pdb title:  
Cryo-em structure of human pyruvate carboxylase with acetyl-coa In the ground
state [more info...]  
  
Chain information for 7wtc.pdb #2  
---  
Chain | Description | UniProt  
A | pyruvate carboxylase, mitochondrial | PYC_HUMAN  
B | pyruvate carboxylase, mitochondrial | PYC_HUMAN  
C D | pyruvate carboxylase, mitochondrial | PYC_HUMAN  
  
Non-standard residues in 7wtc.pdb #2  
---  
ACO — acetyl coenzyme *A  
BTI — 5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal  
  

> hide #!1 models

> hide #2 models

> show #2 models

> hide #!3 models

> show #4 models

> ui tool show Matchmaker

> matchmaker #2 to #4

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 PC-final-coot-1.pdb, chain A (#4) with 7wtc.pdb, chain B (#2),
sequence alignment score = 3239  
RMSD between 526 pruned atom pairs is 1.149 angstroms; (across all 684 pairs:
15.426)  
  

> open "E:/sui lab/CC/MCC_science_report/new pdbs/PC-state2-final.pdb"

Chain information for PC-state2-final.pdb #5  
---  
Chain | Description  
A B C D | No description available  
  

> hide #4 models

> ui tool show Matchmaker

> matchmaker #!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 7wtc.pdb, chain B (#2) with PC-state2-final.pdb, chain A (#5),
sequence alignment score = 5031.8  
RMSD between 497 pruned atom pairs is 1.138 angstroms; (across all 1058 pairs:
14.711)  
  

> color #2 #ebcbb5 transparency 0

> color #2 #ebbaa1 transparency 0

> color #2 #ebcf9f transparency 0

> color #5 #af83fa transparency 0

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> hide #2 models

> show #2 models

> hide #!5 models

> select #2/D,C:495-1091

9208 atoms, 9428 bonds, 1194 residues, 1 model selected  

> transparency sel 90 target c

> select up

9560 atoms, 9790 bonds, 1239 residues, 1 model selected  

> select #2/A,B:495-1091

9208 atoms, 9428 bonds, 1194 residues, 1 model selected  

> transparency sel 90 target c

> hide sel atoms

> select clear

> show #!5 models

> hide #2 models

> show #2 models

> select #5/A,B,C,D:495-1091

18416 atoms, 18852 bonds, 2388 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #5/A,B,C,D:495-1091

18416 atoms, 18852 bonds, 2388 residues, 1 model selected  

> transparency sel 100 target c

> select #2/A,B:495-1091

9208 atoms, 9428 bonds, 1194 residues, 1 model selected  

> transparency sel 100 target c

> select #2/D,C:495-1091

9208 atoms, 9428 bonds, 1194 residues, 1 model selected  

> transparency sel 100 target c

> select clear

> select #2/D,C:495-1091

9208 atoms, 9428 bonds, 1194 residues, 1 model selected  

> transparency sel 90 target c

> select #2/A,B:495-1091

9208 atoms, 9428 bonds, 1194 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #5/A,B,C,D:495-1091

18416 atoms, 18852 bonds, 2388 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #2/A,C:1092-1178

1302 atoms, 1318 bonds, 174 residues, 1 model selected  

> transparency sel 90 target c

> select #5/B,D:1092-1178

1250 atoms, 1262 bonds, 2 pseudobonds, 168 residues, 2 models selected  

> transparency sel 90 target c

> select clear

> hide #2#!5 atoms

> select ::name="ACO"

102 atoms, 106 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 102 atom styles  

> color sel byhetero

> select ::name="BTI"

120 atoms, 128 bonds, 8 residues, 2 models selected  

> show sel & #2 atoms

> style sel & #2 ball

Changed 60 atom styles  

> color sel & #2 byhetero

> transparency sel 50 target a

> select clear

> save "E:/sui lab/CC/MCC_science_report/new pdbs/figure/PC-align.jpg" width
> 1336 height 776 supersample 3

> save "E:/sui lab/CC/MCC_science_report/new pdbs/pse and cxs/PCalign.cxs"

——— End of log from Thu Nov 24 20:35:17 2022 ———

opened ChimeraX session  

> open "E:/sui lab/CC/MCC_science_report/new pdbs/PC-state2-final-coot-3.pdb"

Chain information for PC-state2-final-coot-3.pdb #6  
---  
Chain | Description  
A B C D | No description available  
  

> ui tool show Matchmaker

> matchmaker #!6 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PC-state2-final.pdb, chain A (#5) with PC-state2-final-coot-3.pdb,
chain A (#6), sequence alignment score = 4637.6  
RMSD between 681 pruned atom pairs is 0.219 angstroms; (across all 939 pairs:
3.834)  
  

> hide #2 models

> show #2 models

> hide #!5 models

> color #6 #b16cff transparency 0

> select #5/A,C,B,D:493-1090

18440 atoms, 18876 bonds, 2392 residues, 1 model selected  

> select #6/A,C,B,D:493-1090

18440 atoms, 18876 bonds, 2392 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> select #6/A,C,B,D:1092-1178

2608 atoms, 2640 bonds, 348 residues, 1 model selected  

> transparency sel 90 target c

> select #2/A,C,B,D:1092-1178

2604 atoms, 2636 bonds, 348 residues, 1 model selected  

> transparency sel 90 target c

> select clear

> save "E:/sui lab/CC/MCC_science_report/new pdbs/figure/pc5.jpg" width 1336
> height 776 supersample 3

> save "E:/sui lab/CC/MCC_science_report/new pdbs/pse and cxs/PCalign.cxs"

——— End of log from Sun Nov 27 19:32:21 2022 ———

opened ChimeraX session  

> open "E:/sui lab/CC/MCC_science_report/new
> pdbs/map/J380_006_volume_map_whole_pc.mrc"

Opened J380_006_volume_map_whole_pc.mrc as #7, grid size 320,320,320, pixel
1.1, shown at level 0.103, step 2, values float32  

> hide #!7 models

> show #!7 models

> hide #2 models

> color #7 #cbcbcb models transparency 0

> color #7 #b9b9b9 models transparency 0

> transparency #7.1 50

> color #7 #aaaaff models transparency 0

> transparency #7.1 50

> color #7 #aa55ff models transparency 0

> transparency #7.1 50

> show #2 models

> hide #2 models

> hide #!7 models

> show #!7 models

> transparency #7.1 0

> select #7

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,-0.69059,0,1,0,0.077153,0,0,1,20.58

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.93465,0.34849,-0.07063,-38.021,-0.10368,0.077101,-0.99162,354.6,-0.34012,0.93414,0.10819,72.892

> view matrix models
> #7,-0.1994,0.97291,-0.11698,59.646,-0.11672,-0.14211,-0.98294,393.88,-0.97294,-0.18235,0.1419,374.26

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.1994,0.97291,-0.11698,56.557,-0.11672,-0.14211,-0.98294,393.15,-0.97294,-0.18235,0.1419,360.67

> view matrix models
> #7,-0.1994,0.97291,-0.11698,57.133,-0.11672,-0.14211,-0.98294,379.25,-0.97294,-0.18235,0.1419,353.45

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.073875,0.99372,0.084015,-3.8814,-0.063985,0.079348,-0.99479,333.17,-0.99521,-0.078866,0.057722,353.97

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.073875,0.99372,0.084015,5.1571,-0.063985,0.079348,-0.99479,345.85,-0.99521,-0.078866,0.057722,356.84

> ~select #7

Nothing selected  

> ui tool show "Fit in Map"

Fit molecule PC-state2-final-coot-3.pdb (#6) to map
J380_006_volume_map_whole_pc.mrc (#7) using 29128 atoms  
average map value = 0.1816, steps = 88  
shifted from previous position = 6.17  
rotated from previous position = 7.48 degrees  
atoms outside contour = 9121, contour level = 0.10254  
  
Position of PC-state2-final-coot-3.pdb (#6) relative to
J380_006_volume_map_whole_pc.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.99998614 0.00438867 0.00290973 349.89875470  
0.00439240 0.99998954 0.00127731 -1.19361239  
-0.00290409 0.00129007 -0.99999495 351.60677644  
Axis 0.00219527 0.99999738 0.00064182  
Axis point 175.20621173 0.00000000 175.54948809  
Rotation angle (degrees) 179.83344569  
Shift along axis -0.19981582  
  

> show #2 models

> transparency #7.1 50

> color #7 white models transparency 0

> transparency #7.1 50

> color #7 #cecece models transparency 0

> color #7 #c6c6c6 models transparency 0

> color #7 #cbcbcb models transparency 0

> transparency #7.1 50

> transparency sel 90 target s

> select #7

2 models selected  

> transparency sel 90 target s

> ~select #7

Nothing selected  

> lighting soft

> hide #!7 models

> show #!7 models

> hide #!7 models

> lighting soft

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> show #!7 models

> hide #!7 models

> show #!7 models

> ui tool show Matchmaker

> matchmaker #2 to #6

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 PC-state2-final-coot-3.pdb, chain A (#6) with 7wtc.pdb, chain B
(#2), sequence alignment score = 4363.4  
RMSD between 530 pruned atom pairs is 1.154 angstroms; (across all 942 pairs:
16.393)  
  

> hide #!7 models

> cartoon style #2,6 modeHelix tube sides 20

> select #2

28418 atoms, 29052 bonds, 3667 residues, 1 model selected  

> transparency sel 0 target c

> ~select #2

Nothing selected  

> select #6

29128 atoms, 29772 bonds, 4 pseudobonds, 3768 residues, 2 models selected  

> transparency sel 0 target c

> ~select #6

Nothing selected  

> show #!7 models

> transparency sel 80 target s

> transparency sel 70 target s

> select #7

2 models selected  

> transparency sel 70 target s

> ~select #7

Nothing selected  

> lighting soft

> lighting flat

> lighting full

> lighting soft

[Repeated 1 time(s)]

> volume #7 step 1

> volume #7 level 0.03458

> ui tool show "Hide Dust"

> surface dust #7 size 10.16

> surface dust #7 size 11.93

[Repeated 1 time(s)]

> volume #7 level 0.05409

> volume #7 level 0.03978

> save "E:/sui lab/CC/MCC_science_report/20230921-new/PC-whole.cxs"

——— End of log from Sat Sep 23 17:14:46 2023 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 517.00
OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82AX
OS: Microsoft Windows 10 家庭中文版 (Build 19044)
Memory: 17,040,195,584
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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 pett, 2 years ago

Component:	Unassigned → Graphics
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → OpenGL texture was not deleted before graphics.Texture destroyed

comment:2 by Tom Goddard, 2 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed
Summary:	OpenGL texture was not deleted before graphics.Texture destroyed → Crashed in Qt event loop after opening a session

Crashed in Qt event loop after opening a session. No clues.

When this session was created there was a traceback in the middle "OpenGL texture was not deleted before graphics.Texture destroyed" indicating something went wrong with clean up of a model, probably volume data. But I don't think it has anything to do with the crash.

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