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Opened 3 years ago
Closed 3 years ago
#7485 closed defect (duplicate)
Surface.vertices is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-124-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open projeto.csx.cxs
Log from Tue Aug 16 20:21:47 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 fuzja.pdb
Summary of feedback from opening fuzja.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-06-02 Time 15:26:10 CEST +0200 (1654176370.09 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/ania_k/Phenix_output/resolutions-
diff/195A/fuzja_1_18_I.mtz
45 messages similar to the above omitted
Chain information for fuzja.pdb #1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> hide atoms
> lighting soft
> graphics silhouettes true
> ui tool show "Color Actions"
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) #204a87ff
> select clear
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> color sel dark gray
> select clear
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark gray
> color sel dim gray
> color sel #888a85ff
> color sel #555753ff
> color sel #888a85ff
[Repeated 2 time(s)]
> select clear
> view
> select #1/A ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel surfaces
> hide sel surfaces
> surface #1/A ::name="SAM" resolution 2.3
1 Gaussian surfaces, threshold level 1.332
> surface #1/A ::name="SAM" resolution 2.4
1 Gaussian surfaces, threshold level 1.163
> color (#!1 & sel) orange red
> select clear
> select #1/B ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel atoms
> surface #1/B ::name="SAM" resolution 2.4
1 Gaussian surfaces, threshold level 1.163
> color sel orange red
> select clear
> view
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> select #1/A ::name="MG"
Nothing selected
> show atoms
> hide atoms
> select #1/A ::name="MG"
Nothing selected
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 2 atom styles
> select ::name="MG" size atomRadius +.5
Expected a keyword
> size atomRadius +.5
Changed 7589 atom radii
> size atomRadius +1
Changed 7589 atom radii
> select clear
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG_1.png
> width 3000 height 2097 supersample 3 transparentBackground true
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> color sel purple
> ui tool show "Color Actions"
> color sel #8e40bfff
> color sel #9940bfff
> color sel #a840bfff
> color sel #ac55bfff
> color sel #7a3c87ff
> color sel #7a3e87ff
> color sel #7d408bff
> color sel #7f4a8bff
> color sel #8d529aff
> color sel #8d559aff
> color sel #9358a0ff
> color sel #9359a0ff
> color sel #9c5faaff
> color sel #9d60aaff
> color sel #a163afff
> color sel #a967b8ff
> color sel #a861b8ff
> color sel #b066c0ff
> color sel #af5fc0ff
> color sel #b664c9ff
> color sel #b864caff
[Repeated 1 time(s)]
> color sel #b658caff
> color sel #bd5cd2ff
> color sel #bb53d2ff
> color sel #bc54d3ff
> color sel #bb4dd3ff
> color sel #ad47c4ff
> color sel #aa35c4ff
> color sel #a333bcff
> color sel #a32fbcff
> color sel #a22fbbff
[Repeated 1 time(s)]
> color sel #a02fb8ff
> color sel #a134b8ff
> color sel #9530abff
> color sel #9637abff
> color sel #8f34a3ff
> color sel #903aa3ff
> color sel #8f3aa2ff
> color sel #8f3ba2ff
[Repeated 1 time(s)]
> color sel #8e3ba1ff
> color sel #9042a1ff
> color sel #8d409dff
> color sel #8e499dff
> color sel #924ba2ff
> color sel #924ca2ff
> color sel #944da3ff
> color sel #954ea4ff
> color sel #954fa4ff
> color sel #9653a4ff
> color sel #9251a1ff
> color sel #9458a1ff
> color sel #8f559cff
> color sel #90599cff
> color sel #8d5799ff
> color sel #8d5899ff
> color sel #8e589aff
> color sel #8e599aff
[Repeated 1 time(s)]
> color sel #905a9cff
> color sel #9b61a7ff
> color sel #9543a7ff
> color sel #813a91ff
> color sel #7f3091ff
> color sel #813192ff
> color sel #802b92ff
[Repeated 1 time(s)]
> color sel #802c93ff
> color sel #812f93ff
> color sel #863198ff
> color sel #883d98ff
> color sel #9141a2ff
> color sel #9144a2ff
> color sel #9344a4ff
[Repeated 2 time(s)]
> select clear
> select #1/A :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> select #1/A :85-129 :354-397
733 atoms, 746 bonds, 89 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #eeeeecff
> color sel #555753ff
> color sel #2e3436ff
> color sel #c4a000ff
> color sel #ce5c00ff
> color sel #f57900ff
> color sel #fcaf3eff
> color sel #4e9a06ff
> select #1/A :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> rainbow #1/A :85-129 palette rainbow
> rainbow #1/A :354-397 palette rainbow
> rainbow #1/B :354-397 palette rainbow
> rainbow #1/B :85-129 palette rainbow
> select clear
> select #1/B ::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> surface #1/B ::name="SAM" resolution 2.4
1 Gaussian surfaces, threshold level 1.163
> surface #1/B ::name="SAM" resolution 0.1
Unable to allocate 48.5 GiB for an array with shape (3198, 1320, 3086) and
data type float32
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG_1.png
> width 3500 height 2447 supersample 4 transparentBackground true
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/mono_SAM_SAM_MG.png width
> 35000 height 24466 supersample 4 transparentBackground true
Image size 35000 x 24466 too large, exceeds maximum OpenGL render buffer size
32768
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/mono_SAM_SAM_MG_1.png
> width 3000 height 2097 supersample 4 transparentBackground true
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/mono_SAM_SAM_MG_1.png
> width 3500 height 2447 supersample 3 transparentBackground true
> select #1/A :167 : 168 :176
27 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 27 atom styles
> style sel sphere
Changed 27 atom styles
> style sel ball
Changed 27 atom styles
> color sel byhetero
> select clear
> select /A:167@OE1
1 atom, 1 residue, 1 model selected
> select /C:2@MG
1 atom, 1 residue, 1 model selected
> select add /A:167@OE1
2 atoms, 2 residues, 1 model selected
> select subtract /A:167
1 atom, 1 residue, 1 model selected
> select add /A:167@OE1
2 atoms, 2 residues, 1 model selected
> select clear
> select #1/A :167 : 168 :176 #1/B :115
36 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> hide cartoons
> select /A:167@O
1 atom, 1 residue, 1 model selected
> select add /C:2@MG
2 atoms, 2 residues, 1 model selected
> ui tool show Contacts
> contacts
9 contacts
> contacts color #edd400
9 contacts
> select clear
> select #1/A :167 : 168 :176 #1/B :115
36 atoms, 33 bonds, 4 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select clear
> show cartoons
> select /C:2@MG
1 atom, 1 residue, 1 model selected
> select add /A:167
10 atoms, 8 bonds, 2 residues, 1 model selected
> ui tool show Contacts
> contacts color #edd400
9 contacts
> ui tool show Distances
Exactly two atoms must be selected!
> select subtract /A:167
1 atom, 1 residue, 1 model selected
> select add /A:167
10 atoms, 8 bonds, 2 residues, 1 model selected
> select clear
> select /A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add /C:2@MG
1 atom, 1 residue, 1 model selected
> select add /A:167
10 atoms, 8 bonds, 2 residues, 1 model selected
> contacts continuous true
9 contacts
> contacts color #ffffff
9 contacts
> select #1/A :167 : 168 :176 #1/B :115
36 atoms, 33 bonds, 4 residues, 1 model selected
> contacts overlapCutoff 0.1 color #ffffff
No contacts
> contacts overlapCutoff 0.1 color #ffffff
No contacts
> ~contacts
> select clear
> select /A:167@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 5 atoms, 11 residues, 4 bonds
> hide sel atoms
> select clear
> select /C:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG_1.png
> width 3500 height 1706 supersample 4 transparentBackground true
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/mono_SAM_SAM_MG_1.png
> width 3500 height 1706 supersample 4 transparentBackground true
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> show sel cartoons
> select clear
> view orient
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> ui tool show "Model Panel"
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/dimer_SAM_SAM_MG_1.png
> width 3500 height 2104 supersample 4 transparentBackground true
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/mono_SAM_SAM_MG_1.png
> width 3500 height 2104 supersample 4 transparentBackground true
> ui tool show "File History"
> ui tool show "Model Panel"
> ui tool show Toolbar
> select #1/A :115 #1/B :167 :168 :176
36 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> hide cartoons
> hide surfaces
> select #1/A :115 #1/B :167 :168 :176
36 atoms, 33 bonds, 4 residues, 1 model selected
> color sel byhetero
> select clear
> ui tool show Contacts
> contacts overlapCutoff 0.5 color #ffffff
No contacts
> contacts overlapCutoff 0.5 color #ffffff
No contacts
> select #1/A :115 #1/B :167 :168 :176
36 atoms, 33 bonds, 4 residues, 1 model selected
> contacts overlapCutoff 0.5 color #ffffff
No contacts
> select clear
> ui tool show Distances
> select /A:115@OE1
1 atom, 1 residue, 1 model selected
> select add /C:1@MG
2 atoms, 2 residues, 1 model selected
> distance /A:115@OE1 /C:1@MG
Distance between /A GLU 115 OE1 and /C MG 1 MG: 2.735Å
> select /B:176@OE2
1 atom, 1 residue, 1 model selected
> select add /C:1@MG
2 atoms, 2 residues, 1 model selected
> distance /B:176@OE2 /C:1@MG
Distance between /B GLU 176 OE2 and /C MG 1 MG: 2.209Å
> select /B:167@O
1 atom, 1 residue, 1 model selected
> select add /C:1@MG
2 atoms, 2 residues, 1 model selected
> distance /B:167@O /C:1@MG
Distance between /B GLU 167 O and /C MG 1 MG: 2.273Å
> select clear
> select ::name="HOH"
729 atoms, 729 residues, 1 model selected
> show sel atoms
> select clear
> select /S:29@O
1 atom, 1 residue, 1 model selected
> ui tool show "Model Panel"
> ui tool show "Command Line Interface"
> ui tool show Log
> select clear
> select /S:29@O
1 atom, 1 residue, 1 model selected
> select ::name="HOH"
729 atoms, 729 residues, 1 model selected
> hide sel atoms
> select /S:29@O
1 atom, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /S:29@O
1 atom, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
> select add /S:29@O
1 atom, 1 residue, 1 model selected
> select add /C:1@MG
2 atoms, 2 residues, 1 model selected
> distance /S:29@O /C:1@MG
Distance between /S HOH 29 O and /C MG 1 MG: 2.203Å
> distance style symbol false
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style decimalPlaces 0
> distance style radius 0.09
> distance style radius 0.08
> distance style dashes 8
> distance style dashes 7
> distance style dashes 6
> distance style dashes 5
> distance style dashes 4
> distance style dashes 3
> distance style dashes 4
> distance style dashes 5
> distance style dashes 6
> distance style dashes 7
> distance style dashes 8
> select /B:176@OE2
1 atom, 1 residue, 1 model selected
> distance style decimalPlaces 3
> distance style dashes 9
> distance style radius 0.1
> distance style symbol true
> distance style symbol false
> distance style number false
Expected a keyword
> distance style color #06427a
> distance style color #3465a4
> distance style color #729fcf
> distance style color #73d216
> distance style color #4e9a06
> distance style color #c4a000
> distance style color #ce5c00
> distance style color #f57900
> distance style color #edd400
> distance style color #fce94f
> distance style color #edd400
> ui mousemode right "resize markers"
> ui mousemode right "move markers"
> ui mousemode right label
> ui autostart true Distances
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style symbol true
> distance style symbol false
> label defaultHeight 0.69
> label defaultHeight 0.6799999999999999
> label defaultHeight 0.67
> label defaultHeight 0.66
> label defaultHeight 0.65
> label defaultHeight 0.64
> label defaultHeight 0.63
> label defaultHeight 0.62
> label defaultHeight 0.61
> label defaultHeight 0.6
> distance style symbol true
> distance style symbol false
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/projeto.csx.cxs
——— End of log from Tue Aug 16 20:21:47 2022 ———
opened ChimeraX session
Drag select of 37 atoms, 33 bonds, 4 pseudobonds
Drag select of 38 atoms, 33 bonds, 4 pseudobonds
> hide sel atoms
> select clear
> show cartoons
> rainbow #1/B :376-382
> undo
> select #1/B :376-382
54 atoms, 55 bonds, 7 residues, 1 model selected
> select #1/B :376-382 #1/A :376:382
65 atoms, 65 bonds, 9 residues, 1 model selected
> select ~sel
7524 atoms, 6935 bonds, 6 pseudobonds, 1574 residues, 4 models selected
> hide sel cartoons
> select #1/B :376-382 #1/A :376-382
108 atoms, 110 bonds, 14 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/B :376-382 #1/A :376-382
108 atoms, 110 bonds, 14 residues, 1 model selected
> select ~sel
7481 atoms, 6890 bonds, 6 pseudobonds, 1569 residues, 4 models selected
> show sel cartoons
> color (#!1 & sel) light gray
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1344, in <lambda>
cmd="color %%s %s" % spaced_name: run(cmd))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1504, in _run_surf_command
run(self.session, cmd % selector)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 127, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 361, in _set_surface_colors
ns = _color_surfaces_at_atoms(atoms, color.uint8x4(), opacity=opacity,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 1258, in
_color_surfaces_at_atoms
s.color_atom_patches(atoms, color, per_atom_colors, opacity = opacity)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 418, in color_atom_patches
v, all_atoms = self._vertices_for_atoms(atoms)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
See log for complete Python traceback.
> select clear
> select #1/B :376-382 #1/A :376-382
108 atoms, 110 bonds, 14 residues, 1 model selected
> select ~sel
7481 atoms, 6890 bonds, 6 pseudobonds, 1569 residues, 4 models selected
> color (#!1 & sel) white
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1344, in <lambda>
cmd="color %%s %s" % spaced_name: run(cmd))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1504, in _run_surf_command
run(self.session, cmd % selector)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 127, in color
ns = _set_surface_colors(session, satoms, color, opacity, bgcolor,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 361, in _set_surface_colors
ns = _color_surfaces_at_atoms(atoms, color.uint8x4(), opacity=opacity,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 1258, in
_color_surfaces_at_atoms
s.color_atom_patches(atoms, color, per_atom_colors, opacity = opacity)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 418, in color_atom_patches
v, all_atoms = self._vertices_for_atoms(atoms)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molsurf.py", line 320, in _vertices_for_atoms
nv = len(self.vertices)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MSI
Model: MS-7A70
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 5.4Gi 17Gi 86Mi 8.5Gi 25Gi
Swap: 7.6Gi 0B 7.6Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)
Subsystem: PNY GP104 [GeForce GTX 1070] [196e:119d]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
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-Cytoscape: 0.1
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-LinuxSupport: 1.0
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-NIHPresets: 1.0.6
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: 1.2.1
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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
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
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.4
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
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Surface.vertices is None |
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Reported by Fernando Bruno da Silva