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Opened 23 months ago
Closed 23 months ago
#10284 closed defect (can't reproduce)
Color surface: object of type 'NoneType' has no len()
| 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-5.4.0-167-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 /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/new_figures.cxs
> format session
Log from Wed Aug 24 19:02:44 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 /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/fuzja.pdb format pdb
Summary of feedback from opening /home/users/fbruno/Postdoc/Projeto-TrmD-
Tm1570/Crystal_Strcuture/Structures/Crystal/dimer/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
Drag select of 534 atoms, 844 residues, 2 pseudobonds, 458 bonds
> hide sel atoms
> select #1/B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> color (#!1 & sel) light gray
> select #1/A
3532 atoms, 3609 bonds, 437 residues, 1 model selected
> color sel gray
> color sel dim gray
> select clear
> select #1/B :352-397
367 atoms, 374 bonds, 46 residues, 1 model selected
> color sel orange
> set bgColor white
> graphics silhouettes true
> lighting soft
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting soft
> select clear
> select #1/A :352-397
371 atoms, 378 bonds, 46 residues, 1 model selected
> color sel orange
> select clear
> select #1/B :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> color sel blue
> select #1/A :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> color sel blue
> select clear
> cartoon style strand xsection rectangle width 4
> cartoon style strand xsection rectangle width 3
> cartoon style helix width 2.5 thickness 0.8
> select #1/B/A :85-129
3704 atoms, 3775 bonds, 2 pseudobonds, 460 residues, 2 models selected
> select #1/B #1/A :85-129
3704 atoms, 3775 bonds, 2 pseudobonds, 460 residues, 2 models selected
> select #1/B :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #406abfff
> color sel #0040bfff
> color sel #003399ff
[Repeated 3 time(s)]
> color sel #bf4040ff
> color sel #003399ff
> select #1/A :85-129
378 atoms, 384 bonds, 45 residues, 1 model selected
> color sel #bf4040ff
> color sel #003399ff
> select clear
> view
> ui tool show "Side View"
> ui tool show "Model Panel"
> view
> cofr frontCenter
> ui tool show Toolbar
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/dimer_chainA_chainB_2_cartoon.png
> width 3500 height 2447 supersample 4 transparentBackground true
> select #1/A :85-129 #1/B :85-129
756 atoms, 768 bonds, 90 residues, 1 model selected
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 182 residues, 1 model selected
> select ~sel
6095 atoms, 5480 bonds, 2 pseudobonds, 1401 residues, 2 models selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select clear
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> cartoon style xsection oval modeHelix default
> cartoon style xsection rectangle modeHelix default
> cartoon style coil xsection oval
> cartoon style xsection barbell modeHelix default
> cartoon style modeHelix tube sides 20
> hide cartoons
> show atoms
> style stick
Changed 7589 atom styles
> style sphere
Changed 7589 atom styles
> style ball
Changed 7589 atom styles
> hide (protein|nucleic) target a
> cartoon hide
> show backbone target ab
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> select clear
[Repeated 1 time(s)]Drag select of 1706 atoms, 136 bonds, 840 pseudobonds
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 178 pseudobonds, 182 residues, 2 models selected
> select #1/A #1/B
6858 atoms, 7000 bonds, 842 pseudobonds, 852 residues, 3 models selected
> select ~sel
731 atoms, 731 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 178 pseudobonds, 182 residues, 2 models selected
> cartoon (#!1 & sel)
> show sel cartoons
> cartoon style sel xsection oval modeHelix default
> select clear
> size atomRadius +2
Changed 7589 atom radii
> size atomRadius +0.5
Changed 7589 atom radii
> select clear
[Repeated 1 time(s)]Drag select of 6 atoms, 5 bonds
> hide sel atoms
> select clear
Drag select of 6 atoms, 5 bonds
> hide sel atoms
Drag select of 5 atoms, 7 pseudobonds
> select clear
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> select clear
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> show sel surfaces
> select clear
> surface resolution 20
2 Gaussian surfaces, threshold level 0.023
> undo
> hide sel surfaces
[Repeated 1 time(s)]
> show sel surfaces
> surface off
Expected an atoms specifier or a keyword
> hide surfaces
> show sel cartoons
> hide sel cartoons
> hide sel surfaces
[Repeated 3 time(s)]Drag select of fuzja.pdb_A Gaussian surface, 11118 of
14604 triangles, fuzja.pdb_B Gaussian surface, 10490 of 14448 triangles, 599
atoms, 174 residues, 118 bonds, 480 pseudobonds
> surface resolution 1
2 Gaussian surfaces, threshold level 15.516 - 15.519
> surface resolution 0
> select clear
> show surfaces
> hide surfaces
> select clear
[Repeated 1 time(s)]
> hide surfaces
> show surfaces
[Repeated 1 time(s)]
> hide surfaces
> show surfaces
> hide surfaces
> surface resolution 0.1
Unable to allocate 1.50 TiB for an array with shape (8280, 7056, 7043) and
data type float32
> surface ::name="SAM" resolution 2
2 Gaussian surfaces, threshold level 1.970 - 1.971
> surface ::name="SAM" resolution 5
2 Gaussian surfaces, threshold level 0.235 - 0.237
> surface ::name="SAM" resolution 0
> surface ::name="SAM" resolution 4
2 Gaussian surfaces, threshold level 0.348
> surface ::name="SAM" resolution 3.5
2 Gaussian surfaces, threshold level 0.449 - 0.450
> surface ::name="SAM" resolution 2
2 Gaussian surfaces, threshold level 1.970 - 1.971
> surface ::name="SAM" resolution 3
2 Gaussian surfaces, threshold level 0.640 - 0.643
> surface ::name="SAM" resolution 2.5
2 Gaussian surfaces, threshold level 1.040 - 1.052
> surface ::name="SAM" resolution 2.4
2 Gaussian surfaces, threshold level 1.163
> select clear
> surface ::name="SAM" resolution 2.4 style dot
Expected a keyword
> surface style dot ::name="SAM" resolution 2.4
Expected fewer arguments
> surface ::name="SAM" resolution 2.4
2 Gaussian surfaces, threshold level 1.163
> surface ::name="SAM" style dt
Expected a keyword
> surface ::name="SAM" style dot
Expected a keyword
> surface ::name="SAM" style dote
Expected a keyword
> surface ::name="SAM" style mesh
Expected a keyword
> surface ::name="SAM" cap false
Expected a keyword
> surface cap false
> surface mesh
Expected an atoms specifier or a keyword
> surface style mesh
> surface style dot
> surface style mesh
> surface style dot
> surface style solid
> surface ::name="SAM"
> select ::name="SAM"
108 atoms, 116 bonds, 4 residues, 1 model selected
> select #1/A::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> color (#!1 & sel) #cc0000ff
> color (#!1 & sel) #ef2929ff
> color (#!1 & sel) #ce5c00ff
> color (#!1 & sel) #a40000ff
> color (#!1 & sel) #bf5454ff
> color (#!1 & sel) #934141ff
> color (#!1 & sel) #934444ff
> color (#!1 & sel) #a24a4aff
> color (#!1 & sel) #a24545ff
> color (#!1 & sel) #b95050ff
> color (#!1 & sel) #b94b4bff
> color (#!1 & sel) #c14e4eff
> color (#!1 & sel) #c14d4dff
> color (#!1 & sel) #c95050ff
> color (#!1 & sel) #c93b3bff
> color (#!1 & sel) #dd4141ff
> color (#!1 & sel) #dd3c3cff
> color (#!1 & sel) #e73e3eff
> color (#!1 & sel) #3ee741ff
> color (#!1 & sel) #3ee771ff
> color (#!1 & sel) #3ee793ff
> color (#!1 & sel) #3ee7b9ff
> color (#!1 & sel) #3ee7bcff
> color (#!1 & sel) #3ee7caff
> color (#!1 & sel) #3ec0e7ff
> color (#!1 & sel) #3ea4e7ff
> color (#!1 & sel) #3ea8e7ff
> color (#!1 & sel) #3ee7e5ff
> color (#!1 & sel) #3ee5e7ff
> color (#!1 & sel) #3ea4e7ff
> color (#!1 & sel) #3e93e7ff
> select #1/A::name="SAM 801"
Nothing selected
> select #1/A::name="SAM 501"
Nothing selected
> color #3f93e7ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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.
> color #306faeff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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.
> color #3070b0ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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.
> color #3f78b0ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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.
> color #4889caff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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 #1/A::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> color (#!1 & sel) #4e48caff
> color (#!1 & sel) #8b48caff
> color (#!1 & sel) #a048caff
> color (#!1 & sel) #be48caff
> color (#!1 & sel) #ca48bfff
> color (#!1 & sel) #ca48adff
> color (#!1 & sel) #ca48aaff
> color (#!1 & sel) #ca4898ff
> color (#!1 & sel) #ca4892ff
> color (#!1 & sel) #ca487aff
> color (#!1 & sel) #ca4878ff
> color (#!1 & sel) #ca487dff
> color (#!1 & sel) #ca48a0ff
> color (#!1 & sel) #ca48bfff
> color (#!1 & sel) #ca48c2ff
> color (#!1 & sel) #a348caff
> color (#!1 & sel) #7b48caff
> color (#!1 & sel) #486fcaff
> color (#!1 & sel) #48c9caff
> color (#!1 & sel) #48caacff
> color (#!1 & sel) #48caa9ff
> color (#!1 & sel) #48ca99ff
> color (#!1 & sel) #48ca94ff
> color (#!1 & sel) #48ca77ff
> color (#!1 & sel) #48ca6cff
> color (#!1 & sel) #48ca5aff
> color (#!1 & sel) #49ca48ff
> color (#!1 & sel) #4cca48ff
> color (#!1 & sel) #49ca48ff
> color (#!1 & sel) #48ca7aff
> color (#!1 & sel) #48caa1ff
> color (#!1 & sel) #48cab6ff
> color (#!1 & sel) #48cabeff
> color (#!1 & sel) #48cac1ff
> color (#!1 & sel) #48cac4ff
> color (#!1 & sel) #48b9caff
> color (#!1 & sel) #48b4caff
> color (#!1 & sel) #5cca48ff
> color (#!1 & sel) #5eca48ff
> color (#!1 & sel) #71ca48ff
> color (#!1 & sel) #79ca48ff
> color (#!1 & sel) #b3ca48ff
> color (#!1 & sel) #cabf48ff
> color (#!1 & sel) #caa748ff
> color (#!1 & sel) #caa548ff
> color (#!1 & sel) #ca8848ff
> color (#!1 & sel) #ca8248ff
> color (#!1 & sel) #ca8048ff
> color (#!1 & sel) #ca8548ff
> color (#!1 & sel) #caba48ff
> color (#!1 & sel) #caba49ff
> color (#!1 & sel) #9e9139ff
> color (#!1 & sel) #9e9439ff
> color (#!1 & sel) #9e9229ff
> color (#!1 & sel) #a79a2bff
> color (#!1 & sel) #a79815ff
> color (#!1 & sel) #b4a417ff
> color (#!1 & sel) #b4a30bff
> color (#!1 & sel) #baa90cff
> color (#!1 & sel) #baa800ff
> color (#!1 & sel) #d5c000ff
> color (#!1 & sel) #dac500ff
> color (#!1 & sel) #dac502ff
> color (#!1 & sel) #e2cc02ff
> color (#!1 & sel) #e2cd0bff
> color (#!1 & sel) #e6d00bff
> color (#!1 & sel) #e6d00cff
> color (#!1 & sel) #e7d10cff
> color (#!1 & sel) #e7d10dff
> color (#!1 & sel) #e8d20dff
> color (#!1 & sel) #e8d20fff
> color (#!1 & sel) #e6d10fff
> color (#!1 & sel) #e6d112ff
> color (#!1 & sel) #e1cd12ff
> color (#!1 & sel) #e0cc12ff
> color (#!1 & sel) #e0cc13ff
> color (#!1 & sel) #dac613ff
> color (#!1 & sel) #d9c513ff
> color (#!1 & sel) #c7b511ff
> color (#!1 & sel) #c7b40dff
> color (#!1 & sel) #b2a10bff
> color (#!1 & sel) #b2a10cff
> color (#!1 & sel) #aa9a0bff
> color (#!1 & sel) #a9990bff
> select clear
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 182 residues, 1 model selected
> show sel cartoons
[Repeated 10 time(s)]
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
Drag select of 302 atoms, 659 residues, 180 pseudobonds, 126 bonds
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> undo
[Repeated 5 time(s)]Undo failed, probably because structures have been
modified.
> undo
[Repeated 3 time(s)]
> select clear
> select #1/A #1/B
6858 atoms, 7000 bonds, 2 pseudobonds, 852 residues, 2 models selected
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 178 pseudobonds, 182 residues, 2 models selected
> show sel cartoons
> select clear
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 182 residues, 1 model selected
> select #1/A
3532 atoms, 3609 bonds, 340 pseudobonds, 437 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #555753ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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.
> color (#!1 & sel) #888a85ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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.
> color (#!1 & sel) #555753ff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 1463, in <lambda>
run(ses, "color %s %s" % (sel_or_all(ses, ['atoms', 'bonds']),
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
3326 atoms, 3391 bonds, 316 pseudobonds, 415 residues, 3 models selected
> color sel light gray
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_actions/tool.py", line 59, in <lambda>
button.released.connect(lambda *, clr=spaced_name: self._color(clr))
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_actions/tool.py", line 232, in _color
run(self.session, " ; ".join(commands))
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
[Repeated 1 time(s)]
> select #1/A::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel surfaces
> ui tool show "Color Actions"
> color (#!1 & sel) #c4a000ff
> color (#!1 & sel) #ff9933ff
> color (#!1 & sel) #ac4ba8ff
> color (#!1 & sel) #4059bfff
> color (#!1 & sel) #4044bfff
> color (#!1 & sel) #5040bfff
> color (#!1 & sel) #5340bfff
> color (#!1 & sel) #4082bfff
> color (#!1 & sel) #40aebfff
> color (#!1 & sel) #40bf87ff
> color (#!1 & sel) #40bf85ff
> color (#!1 & sel) #40bf78ff
> color (#!1 & sel) #40bf75ff
> color (#!1 & sel) #40bf66ff
> color (#!1 & sel) #40bf63ff
> color (#!1 & sel) #40bf66ff
> color (#!1 & sel) #40bf6bff
> color (#!1 & sel) #40bf6eff
> select #1/B::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel surfaces
> color (#!1 & sel) #89bf40ff
> color (#!1 & sel) #6fbf40ff
> color (#!1 & sel) #40bf5bff
> color (#!1 & sel) #40bf8fff
> color (#!1 & sel) #40a1bfff
> color (#!1 & sel) #4061bfff
> color (#!1 & sel) #405bbfff
> color (#!1 & sel) #4054bfff
> color (#!1 & sel) #4056bfff
> color (#!1 & sel) #4059bfff
> color (#!1 & sel) #408dbfff
> color (#!1 & sel) #40bfbeff
> color (#!1 & sel) #40bfb1ff
> color (#!1 & sel) #40bfaeff
> color (#!1 & sel) #40bfb1ff
> color (#!1 & sel) #404cbfff
> color (#!1 & sel) #5d40bfff
> color (#!1 & sel) #7440bfff
> color (#!1 & sel) #7a40bfff
> color (#!1 & sel) #b840bfff
> color (#!1 & sel) #bf40adff
> color (#!1 & sel) #bf40aaff
> color (#!1 & sel) #bf40a7ff
> color (#!1 & sel) #bf408eff
> color (#!1 & sel) #bf4086ff
> color (#!1 & sel) #bf4079ff
> color (#!1 & sel) #bf4067ff
> color (#!1 & sel) #bf4069ff
> color (#!1 & sel) #bf409dff
> color (#!1 & sel) #bf40bfff
> color (#!1 & sel) #bd40bfff
> select clear
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> size ::name="MG" atomRadius +0.5
Changed 2 atom radii
> size ::name="MG" atomRadius +2
Changed 2 atom radii
> size ::name="MG" atomRadius +5
Changed 2 atom radii
> ui tool show "Color Actions"
> color sel #bf4c4cff
> color sel #973c3cff
> color sel #974343ff
> color sel #a14747ff
> color sel #a14d4dff
> color sel #ab5252ff
> color sel #ab5c5cff
> color sel #bb6565ff
> color sel #bb6161ff
> color sel #c96868ff
> color sel #c93939ff
> color sel #df3f3fff
> color sel #df2d2dff
> color sel #e62f2fff
> color sel #e62d2dff
> color sel #e62929ff
> color sel #e72a2aff
> color sel #e73a3aff
> color sel #eb3b3bff
> color sel #eb6b6bff
> color sel #e56868ff
> color sel #e57777ff
> color sel #e17575ff
> color sel #e18080ff
> color sel #dc7d7dff
> color sel #da7c7cff
> color sel #807cdaff
> color sel #947cdaff
> color sel #ba7cdaff
> color sel #bc7cdaff
> color sel #be7cdaff
> color sel #cf7cdaff
> color sel #da7cc9ff
> color sel #da7cb0ff
> color sel #da7ca2ff
> color sel #da7c9bff
> color sel #da7c82ff
> color sel #da757bff
> color sel #d77379ff
> color sel #d75c63ff
> color sel #ea646cff
> color sel #ea5a62ff
> color sel #ee5b64ff
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/chains_SAM_MG.png
> width 3500 height 2447 supersample 4 transparentBackground true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting soft
> hide cartoons
> show cartoons
> hide cartoons
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 178 pseudobonds, 182 residues, 2 models selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> hide atoms
> hide cartoons
> select clear
> select #1/A::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> color (#!1 & sel) byhetero
> select clear
> transparency 50
> select clear
Drag select of fuzja.pdb_A SES surface, 11356 of 22582 triangles
> show atoms
> hide atoms
> select clear
> select #1/A::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/SAM1.png width 3500
> height 2447 supersample 4 transparentBackground true
> select #1/B::name="SAM"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel atoms
> color (#!1 & sel) byhetero
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/SAM2.png width 3500
> height 2447 supersample 4 transparentBackground true
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/MG.png width 3500
> height 2447 supersample 4 transparentBackground true
> select clear
Drag select of fuzja.pdb_A SES surface, fuzja.pdb_B SES surface, 110 atoms,
116 bonds
> hide sel atoms
> hide sel surfaces
> select clear
> show atoms
> hide atoms
> select clear
> select #1/A #1/B
6858 atoms, 7000 bonds, 2 pseudobonds, 852 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select #1/A #1/B
6858 atoms, 7000 bonds, 2 pseudobonds, 852 residues, 2 models selected
> show sel cartoons
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select #1/A :352-397 #1/B :352-397 #1/A :85-129 #1/B :85-129
1494 atoms, 1520 bonds, 178 pseudobonds, 182 residues, 2 models selected
> show sel cartoons
> select clear
> select #1/A :106-110 #1/B :106-110
82 atoms, 82 bonds, 10 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> hide cartoons
> hide atoms
> select #1/A :106-110 #1/B :106-110
82 atoms, 82 bonds, 10 residues, 1 model selected
> show sel cartoons
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/bettas_chainA-
> chainB.png width 3500 height 2447 supersample 4 transparentBackground true
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/bettas_chainA-
> chainB_2.png width 3500 height 2447 supersample 4 transparentBackground true
> show cartoons
> select clear
> show cartoons
[Repeated 1 time(s)]
> select clear
> hide cartoons
> select #1/A :376-381 #1/B :376-381
100 atoms, 102 bonds, 12 residues, 1 model selected
> show sel cartoons
> select clear
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/sheet_chainA-
> chainB_2.png width 3500 height 2447 supersample 4 transparentBackground true
> select clear
> show cartoons
> cd /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures
Current working directory is: /home/users/fbruno/Postdoc/Projeto-TrmD-
Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures
> save /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Structures/Crystal/New_figures/new_figures.cxs
——— End of log from Wed Aug 24 19:02:44 2022 ———
opened ChimeraX session
> select /B
3326 atoms, 3391 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select clear
> open /home/users/fbruno/Postdoc/Projeto-TrmD-
> Tm1570/Crystal_Strcuture/Tm1570_unpublished/fwdstrukturatm1570/Tm1570_refine_246.pdb
Summary of feedback from opening /home/users/fbruno/Postdoc/Projeto-TrmD-
Tm1570/Crystal_Strcuture/Tm1570_unpublished/fwdstrukturatm1570/Tm1570_refine_246.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2023-01-08 Time 23:11:14 CET +0100 (1673215874.18 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/anna/Phenix_output/Tm1570-234/Refine_218/Tm1570_refine_data.mtz
35 messages similar to the above omitted
Chain information for Tm1570_refine_246.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> view orient
> select #2/B:8-189
1257 atoms, 1279 bonds, 1 pseudobond, 168 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
Drag select of 26 atoms, 25 bonds
Drag select of 29 atoms, 29 bonds
> hide sel atoms
> select clear
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fuzja.pdb, chain A (#1) with Tm1570_refine_246.pdb, chain A (#2),
sequence alignment score = 850.3
RMSD between 162 pruned atom pairs is 0.558 angstroms; (across all 172 pairs:
1.229)
> view orient
Drag select of 4 residues
> select clear
[Repeated 1 time(s)]Drag select of 1 residues
> select #1/A:224
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:246
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:1-246
1982 atoms, 2021 bonds, 246 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 3 residues
> hide sel cartoons
> open /home/users/fbruno/Downloads/3dcm.pdb
3dcm.pdb title:
Crystal structure of the thermotoga maritima spout family RNA-
methyltransferase protein TM1570 In complex with S-adenosyl-L- methionine
[more info...]
Chain information for 3dcm.pdb #3
---
Chain | Description | UniProt
X | adomet | Y1570_THEMA
Non-standard residues in 3dcm.pdb #3
---
SAM — S-adenosylmethionine
> ui tool show Matchmaker
> matchmaker #3 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 Tm1570_refine_246.pdb, chain A (#2) with 3dcm.pdb, chain X (#3),
sequence alignment score = 503
RMSD between 142 pruned atom pairs is 0.852 angstroms; (across all 169 pairs:
3.022)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
See log for complete Python traceback.
> color #2 #3465a4 transparency 0
> color #3 #f57900 transparency 0
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
See log for complete Python traceback.
> select #1/A:247-431
1469 atoms, 1501 bonds, 185 residues, 1 model selected
> color sel red
> color sel forest green
> select clear
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
> hide sel atoms
> select ::name="HOH"
971 atoms, 971 residues, 3 models selected
> hide sel atoms
> select clear
Drag select of 545 residues, 102 atoms, 1 pseudobonds, 85 bonds
> hide sel atoms
> select clear
> select #1/A:247-431
1469 atoms, 1501 bonds, 185 residues, 1 model selected
> color sel magenta
> ui tool show "Color Actions"
> color sel #bf4d4dff
> color sel #783030ff
> color sel #873636ff
> color sel #873b3bff
> color sel #c45555ff
> color sel #c45757ff
> color sel #c95959ff
> color sel #c95a5aff
> color sel #cc5b5bff
> color sel #cc5858ff
> color sel #ca5858ff
> color sel #ca5f5fff
> color sel #d26363ff
> color sel #d26d6dff
> color sel #dd7373ff
> color sel #dd7c7cff
> color sel #e38080ff
> color sel #e39b9bff
> color sel #f0a4a4ff
> color sel #f0a5a5ff
> color sel #f07c7cff
> color sel #e47676ff
> color sel #e45858ff
> color sel #de5656ff
> color sel #de4343ff
> color sel #e04444ff
> color sel #e03434ff
> color sel #e43434ff
> color sel #e47834ff
> color sel #e48e34ff
> color sel #e4b134ff
> color sel #e4d534ff
> color sel #e4dc34ff
> color sel #dde434ff
> color sel #cbe434ff
> color sel #afe434ff
> color sel #96e434ff
> color sel #6fe434ff
> color sel #44e434ff
> color sel #34e44cff
> color sel #34e473ff
> color sel #34e497ff
> color sel #34e4bbff
> color sel #34e4d0ff
> color sel #34dbe4ff
> color sel #34b7e4ff
> color sel #34a2e4ff
> color sel #3485e4ff
> color sel #3477e4ff
> color sel #347be4ff
> color sel #349ee4ff
> color sel #34c9e4ff
> color sel #34e4dbff
> color sel #34e4beff
> color sel #34e4b7ff
> color sel #34e4b4ff
> color sel #34e497ff
> color sel #34e482ff
> color sel #34e465ff
> color sel #34e450ff
> color sel #34e43aff
> color sel #4be434ff
> color sel #60e434ff
> color sel #6fe434ff
> color sel #84e434ff
> color sel #88e434ff
> color sel #8fe434ff
> color sel #84e434ff
> color sel #4be434ff
> color sel #34e46cff
> color sel #34e4d4ff
> color sel #34c9e4ff
> color sel #346ce4ff
> color sel #3634e4ff
> color sel #7d34e4ff
> color sel #9934e4ff
> color sel #9d34e4ff
> color sel #9934e4ff
> color sel #5634e4ff
> color sel #3934e4ff
> color sel #3437e4ff
> color sel #343ae4ff
> color sel #3634e4ff
> color sel #6f34e4ff
> color sel #9934e4ff
> color sel #cb34e4ff
> color sel #e434d1ff
> color sel #e434c3ff
> color sel #e434b8ff
> color sel #e434b1ff
> color sel #e434a7ff
> color sel #e4349cff
> color sel #e4348eff
> color sel #e4347fff
> color sel #e43478ff
> color sel #e43475ff
> color sel #e4345fff
> color sel #e43455ff
> color sel #e4343fff
> color sel #e43434ff
> color sel #e4343cff
> color sel #e4349cff
> color sel #e434ceff
> color sel #c834e4ff
> color sel #ab34e4ff
> color sel #8834e4ff
> color sel #7634e4ff
> color sel #8851e4ff
> color sel #7d4bd1ff
> color sel #9672d1ff
> color sel #9a76d7ff
> color sel #ac93d7ff
> color sel #b8a6d7ff
> color sel #beb0d7ff
> color sel #c0b2d7ff
> color sel #bfb1d7ff
> color sel #b8a5d7ff
> color sel #b6a4d5ff
> color sel #ab91d5ff
> color sel #a68ed0ff
> color sel #9d7ed0ff
> color sel #987bcaff
> color sel #855ccaff
> color sel #7752b5ff
> color sel #7148b5ff
> color sel #6c45adff
> color sel #6840adff
> color sel #673faaff
> color sel #663eaaff
> color sel #643da7ff
> color sel #633ba7ff
> color sel #603aa2ff
> color sel #6039a2ff
> color sel #563391ff
> color sel #5b3b91ff
> color sel #523583ff
> color sel #553a83ff
> color sel #543981ff
> color sel #563d81ff
> color sel #553c80ff
> color sel #5c4780ff
> color sel #5d4881ff
> color sel #614e81ff
> color sel #68548bff
> color sel #6c598bff
> color sel #7b669eff
> color sel #816f9eff
> color sel #9e89c3ff
> color sel #a390c3ff
> color sel #b09cd3ff
> color sel #b19dd3ff
> color sel #b39fd5ff
> color sel #b29ed5ff
> color sel #9b78d5ff
> color sel #9373caff
> color sel #7b4ccaff
> color sel #7246bbff
> color sel #6634bbff
> color sel #6031b0ff
> color sel #5925b0ff
> color sel #5423a7ff
> color sel #501ca7ff
> color sel #4f1ca6ff
[Repeated 1 time(s)]
> color sel #4d18a6ff
> color sel #4c16a6ff
> color sel #4e17aaff
> color sel #5318b6ff
> color sel #5217b6ff
> color sel #5718c0ff
> color sel #5617c0ff
> color sel #5818c4ff
> color sel #18c3c4ff
> color sel #18c4bfff
> color sel #18c4a3ff
> color sel #18c475ff
> color sel #18c46eff
> color sel #18c464ff
> color sel #16c463ff
> color sel #16c161ff
> color sel #18c162ff
> color sel #1fc166ff
> color sel #1eb962ff
> color sel #26b967ff
> color sel #21a159ff
> color sel #1e9653ff
[Repeated 1 time(s)]
> color sel #1e9452ff
> color sel #1b9450ff
> color sel #188548ff
> color sel #178548ff
> color sel #157841ff
> color sel #157941ff
> color sel #207947ff
> color sel #279155ff
> color sel #3d9162ff
> color sel #46a771ff
> color sel #58a77bff
> color sel #63bd8aff
> color sel #6dbd90ff
> color sel #71c496ff
> color sel #7ac49bff
> color sel #7ecca1ff
> color sel #84cca4ff
> color sel #88d3a9ff
[Repeated 1 time(s)]
> color sel #87d2a8ff
> color sel #79d2a0ff
> color sel #6fd29bff
> color sel #71d59dff
> color sel #61d595ff
> color sel #60d594ff
[Repeated 2 time(s)]
> select clear
> hide #!2 models
> hide #3 models
> show #!2 models
> lighting full depthCue false
> show #3 models
> hide #3 models
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> show #3 models
> hide #!1 models
> show #!1 models
> hide #3 models
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
> show sel & #!1-2 atoms
> select clear
> show #3 models
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
> hide sel atoms
> select clear
> hide #!1 models
> hide #!2 models
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
> show sel & #3 atoms
> show #!2 models
> hide #3 models
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
> show sel & #!2 atoms
Drag select of 25 atoms, 29 bonds
Drag select of 27 atoms, 29 bonds
> hide sel atoms
> select clear
> show #!1 models
> hide #!2 models
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
> show sel & #!1 atoms
> select clear
> select ::name="SAM"
189 atoms, 203 bonds, 7 residues, 3 models selected
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 241, in set_model_color
run(ses, cmd, log=False)
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.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 246, in log_delayed_cmd
Command(ses).run(but.delayed_cmd_text, log_only=True)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.129.03
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 7.1Gi 15Gi 82Mi 8.2Gi 23Gi
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: 1.1.9
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 , 23 months ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Color surface: object of type 'NoneType' has no len() |
comment:2 by , 23 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
The error is because you have a molecular surface that has no vertices. That appears to be because you tried to create a surface at too high a resolution and your computer did not have enough memory
> surface resolution 0.1 Unable to allocate 1.50 TiB for an array with shape (8280, 7056, 7043) and data type float32
I think ChimeraX probably created a surface with no vertices because of this, and later coloring commands then failed.
Current ChimeraX versions (1.7 release candidate is out) don't have this problem. I suggest updating from your old ChimeraX 1.3.
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Reported by Fernando Bruno da Silva