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Opened 5 months ago
Closed 5 months ago
#17666 closed defect (duplicate)
Error setting cavity color
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\Brandon\Downloads\Docking molecular\1js9.pdb" format pdb
1js9.pdb title:
Brome mosaic virus [more info...]
Chain information for 1js9.pdb #1
---
Chain | Description | UniProt
A B C | capsid protein | COAT_BMV 1-189
Non-standard residues in 1js9.pdb #1
---
MG — magnesium ion
P6G — hexaethylene glycol (polyethylene glycol PEG400)
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.5
which is incompatible.
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.2.5 which is incompatible.
\---
pip standard output:
\---
\---
> kvfinder
21 cavities found for 1js9.pdb #1
1js9.pdb Cavities
---
ID | | Volume | Area | Points
1.2.14 | | 1063.58 | 890.11 | 4924
1.2.13 | | 973.3 | 915.24 | 4506
1.2.6 | | 359.42 | 315.71 | 1664
1.2.4 | | 267.41 | 283.72 | 1238
1.2.5 | | 195.7 | 198.56 | 906
1.2.15 | | 102.17 | 88.2 | 473
1.2.2 | | 76.46 | 62.44 | 354
1.2.11 | | 55.08 | 48.53 | 255
1.2.7 | | 53.57 | 68.06 | 248
1.2.3 | | 48.38 | 62.95 | 224
1.2.12 | | 35.42 | 41.34 | 164
1.2.20 | | 27.43 | 33.86 | 127
1.2.16 | | 24.62 | 32.44 | 114
1.2.17 | | 24.62 | 40.68 | 114
1.2.21 | | 21.6 | 29.97 | 100
1.2.10 | | 15.98 | 25.33 | 74
1.2.8 | | 14.69 | 23.26 | 68
1.2.18 | | 13.61 | 15.69 | 63
1.2.9 | | 11.88 | 26.28 | 55
1.2.1 | | 10.8 | 6.97 | 50
1.2.19 | | 8.86 | 18.15 | 41
> view #1.2.14 @< 3.5
> zoom 0.75
moved plane near -50.20387369929432 [-0. -0. -1.]
moved plane far -50.20387369929432 [-0. -0. -1.]
> surface #1.2
> transparency #1.2 50
> ~surface #1.2
> surface #1.2.14
> show #!1 & (#1.2.14 :< 3.5)
> view #1
> view #!1.2.14 @< 3.5
> zoom 0.75
moved plane near -103.85320788225279 [-0. -0. -1.]
moved plane far -103.85320788225279 [-0. -0. -1.]
> ~surface #1.2
[Repeated 1 time(s)]
> surface #!1.2.14
> select #!1.2.14
4924 atoms, 1 residue, 1 model selected
> ~select #!1.2.14
1 model selected
> select #!1.2.14
4924 atoms, 1 residue, 1 model selected
> ~select #!1.2.14
1 model selected
> select #!1 & (#!1.2.14 @< 3.5)
286 atoms, 242 bonds, 64 residues, 1 model selected
> ~select #!1 & (#!1.2.14 @< 3.5)
Nothing selected
> hide #!1 & (#!1.2.14 :< 3.5)
> show #!1 & (#!1.2.14 :< 3.5)
> view #!1.2.13 @< 3.5
> zoom 0.75
moved plane near -101.71983518629101 [-0. -0. -1.]
moved plane far -101.71983518629101 [-0. -0. -1.]
> ~surface #1.2
> surface #!1.2.13
> show #!1 & (#!1.2.13 :< 3.5)
> view #!1.2.14 @< 3.5
> zoom 0.75
moved plane near -103.85320788225279 [-0. -0. -1.]
moved plane far -103.85320788225279 [-0. -0. -1.]
> ~surface #1.2
> surface #!1.2.14
> show #!1 & (#!1.2.14 :< 3.5)
> log
Unknown command: toolshed log
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Find Cavities"
> kvfinder
21 cavities found for 1js9.pdb #!1
1js9.pdb Cavities
---
ID | | Volume | Area | Points
1.3.14 | | 1063.58 | 890.11 | 4924
1.3.13 | | 973.3 | 915.24 | 4506
1.3.6 | | 359.42 | 315.71 | 1664
1.3.4 | | 267.41 | 283.72 | 1238
1.3.5 | | 195.7 | 198.56 | 906
1.3.15 | | 102.17 | 88.2 | 473
1.3.2 | | 76.46 | 62.44 | 354
1.3.11 | | 55.08 | 48.53 | 255
1.3.7 | | 53.57 | 68.06 | 248
1.3.3 | | 48.38 | 62.95 | 224
1.3.12 | | 35.42 | 41.34 | 164
1.3.20 | | 27.43 | 33.86 | 127
1.3.16 | | 24.62 | 32.44 | 114
1.3.17 | | 24.62 | 40.68 | 114
1.3.21 | | 21.6 | 29.97 | 100
1.3.10 | | 15.98 | 25.33 | 74
1.3.8 | | 14.69 | 23.26 | 68
1.3.18 | | 13.61 | 15.69 | 63
1.3.9 | | 11.88 | 26.28 | 55
1.3.1 | | 10.8 | 6.97 | 50
1.3.19 | | 8.86 | 18.15 | 41
> log
Unknown command: toolshed log
> Show nearby residues
Unknown command: Show nearby residues
> log
> log save
Missing or invalid "fileName" argument: Expected a file name
> log save 1
> cd "C:/Users/Brandon/Downloads/Docking molecular"
Current working directory is: C:\Users\Brandon\Downloads\Docking molecular
> log save 1
> kvfinder
21 cavities found for 1js9.pdb #!1
1js9.pdb Cavities
---
ID | | Volume | Area | Points
1.4.14 | | 1063.58 | 890.11 | 4924
1.4.13 | | 973.3 | 915.24 | 4506
1.4.6 | | 359.42 | 315.71 | 1664
1.4.4 | | 267.41 | 283.72 | 1238
1.4.5 | | 195.7 | 198.56 | 906
1.4.15 | | 102.17 | 88.2 | 473
1.4.2 | | 76.46 | 62.44 | 354
1.4.11 | | 55.08 | 48.53 | 255
1.4.7 | | 53.57 | 68.06 | 248
1.4.3 | | 48.38 | 62.95 | 224
1.4.12 | | 35.42 | 41.34 | 164
1.4.20 | | 27.43 | 33.86 | 127
1.4.16 | | 24.62 | 32.44 | 114
1.4.17 | | 24.62 | 40.68 | 114
1.4.21 | | 21.6 | 29.97 | 100
1.4.10 | | 15.98 | 25.33 | 74
1.4.8 | | 14.69 | 23.26 | 68
1.4.18 | | 13.61 | 15.69 | 63
1.4.9 | | 11.88 | 26.28 | 55
1.4.1 | | 10.8 | 6.97 | 50
1.4.19 | | 8.86 | 18.15 | 41
> log save 1.html
> select ::name="LYS"
302 atoms, 268 bonds, 34 residues, 1 model selected
> color sel red
> select ::name="ASP"::name="GLU"
432 atoms, 385 bonds, 50 residues, 1 model selected
> color sel blue
> select clear
> style stick
Changed 51048 atom styles
> style sphere
Changed 51048 atom styles
> style sphere
Changed 51048 atom styles
> style ball
Changed 51048 atom styles
> hide atoms
> show atoms
[Repeated 1 time(s)]
> show cartoons
> hide cartoons
[Repeated 1 time(s)]
> show cartoons
[Repeated 1 time(s)]
> hide cartoons
> show cartoons
> style stick
Changed 51048 atom styles
> style stick
Changed 51048 atom styles
> style sphere
Changed 51048 atom styles
> style ball
Changed 51048 atom styles
> hide atoms
> show atoms
[Repeated 1 time(s)]
> hide atoms
> show atoms
> hide cartoons
> show cartoons
[Repeated 1 time(s)]
> hide cartoons
[Repeated 2 time(s)]
> show cartoons
> show surfaces
[Repeated 1 time(s)]
> hide surfaces
[Repeated 1 time(s)]
> style stick
Changed 51048 atom styles
> style stick
Changed 51048 atom styles
> volume style image
No volumes specified
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume style image
No volumes specified
> volume hide
No volumes specified
> ui mousemode right "link markers"
[Repeated 1 time(s)]
> ui mousemode right "move markers"
> ui mousemode right "link markers"
[Repeated 4 time(s)]
> ui mousemode right "move markers"
> ui mousemode right "delete markers"
[Repeated 1 time(s)]
> nucleotides tube/slab shape ellipsoid
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> log tools
Expected a keyword
> log
[Repeated 1 time(s)]
> log
[Repeated 1 time(s)]
> log tools
Expected a keyword
> contacts
22200 contacts
> contacts
22200 contacts
> style ball
Changed 51048 atom styles
> style stick
Changed 51048 atom styles
> style sphere
Changed 51048 atom styles
> style ball
Changed 51048 atom styles
> style stick
Changed 51048 atom styles
> close session
> cd "C:/Users/Brandon/Downloads/Docking molecular"
Current working directory is: C:\Users\Brandon\Downloads\Docking molecular
> open capsid.pdb
No such file/path: capsid.pdb
> open 1js9.pdb
1js9.pdb title:
Brome mosaic virus [more info...]
Chain information for 1js9.pdb #1
---
Chain | Description | UniProt
A B C | capsid protein | COAT_BMV 1-189
Non-standard residues in 1js9.pdb #1
---
MG — magnesium ion
P6G — hexaethylene glycol (polyethylene glycol PEG400)
> open 8y2d.pdb
8y2d.pdb title:
Cryo-em structure of human dopamine transporter In complex with dopamine [more
info...]
Chain information for 8y2d.pdb #2
---
Chain | Description | UniProt
A | sodium-dependent dopamine transporter | SC6A3_HUMAN 68-620
Non-standard residues in 8y2d.pdb #2
---
CL — chloride ion
LDP — L-dopamine (dopamine)
NA — sodium ion
> open 8y2d.pdb
8y2d.pdb title:
Cryo-em structure of human dopamine transporter In complex with dopamine [more
info...]
Chain information for 8y2d.pdb #3
---
Chain | Description | UniProt
A | sodium-dependent dopamine transporter | SC6A3_HUMAN 68-620
Non-standard residues in 8y2d.pdb #3
---
CL — chloride ion
LDP — L-dopamine (dopamine)
NA — sodium ion
> ui windowfill toggle
[Repeated 1 time(s)]
> hide #!3 models
> show #!2 target m
[Repeated 1 time(s)]
> close #3
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\color_button.py", line 165, in
color_to_numpy_rgba8
if isinstance(color[0], numbers.Integral):
~~~~~^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2111
OpenGL renderer: Intel(R) Iris(R) Plus Graphics 640
OpenGL vendor: Intel
Python: 3.11.4
Locale: es_MX.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Apple Inc.
Model: MacBookPro14,1
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 8,448,602,112
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7360U CPU @ 2.30GHz
OSLanguage: es-MX
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.3
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.39.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.5
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.8.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomlkit: 0.13.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Error setting cavity color |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #16362