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Opened 7 months ago
Closed 6 months ago
#17515 closed defect (duplicate)
Error setting cavity color
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-58-generic-x86_64-with-glibc2.39
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:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
> format session
Log from Thu Apr 24 19:51:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
> format session
Log from Thu Apr 24 18:54:12 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/mu_gpj/cavidade_mu_gpj.cxs
Log from Thu Apr 24 18:35:35 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
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 /home/daniel/chimera/share/chimera/helpdir/UsersGuide/frametut.html
Opened frametut.html
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/chimera_wt.py
Traceback (most recent call last):
File "/home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/chimera_wt.py", line 3,
in <module>
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Error opening python file
/home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/chimera_wt.py
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/chimera_wt.py
Traceback (most recent call last):
File "/home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/chimera_wt.py", line 3,
in <module>
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Error opening python file
/home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/chimera_wt.py
> open /home/daniel/unicamp/EPSPS/ScEPSPS/chimera_mu.py
> close session
mu_model_06.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ScEPSPSm [more info...]
Chain information for mu_model_06.pdb #1
---
Chain | Description
A | No description available
executed chimera_mu.py
> select #1/A
3301 atoms, 3356 bonds, 443 residues, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> 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 #1
17 cavities found for mu_model_06.pdb #1
mu_model_06.pdb Cavities
---
ID | | Volume | Area | Points
1.2.6 | | 570.89 | 591.71 | 2643
1.2.1 | | 131.98 | 132.78 | 611
1.2.4 | | 82.08 | 99.24 | 380
1.2.11 | | 53.35 | 73.2 | 247
1.2.12 | | 41.04 | 61.11 | 190
1.2.2 | | 38.66 | 54.64 | 179
1.2.15 | | 36.72 | 55.37 | 170
1.2.3 | | 27 | 49.65 | 125
1.2.8 | | 26.35 | 44.11 | 122
1.2.5 | | 24.84 | 34.1 | 115
1.2.17 | | 19.01 | 28.29 | 88
1.2.13 | | 12.31 | 29.54 | 57
1.2.16 | | 12.31 | 29.54 | 57
1.2.14 | | 11.45 | 19.17 | 53
1.2.10 | | 11.23 | 21.93 | 52
1.2.7 | | 8.42 | 15.53 | 39
1.2.9 | | 6.48 | 12.8 | 30
> view #1.2.6 @< 3.5
> zoom 0.75
moved plane near -36.59466451377989 [-0.11862448 0.74729734 -0.65381559]
moved plane far -36.59466451377989 [-0.11862448 0.74729734 -0.65381559]
> surface #1.2
> transparency #1.2 50
> ~surface #1.2
> surface #1.2.6
"Nearby" atom/residue distance not valid
> ~surface #1.2
[Repeated 1 time(s)]
> surface #!1.2.6
> ~surface #1.2
[Repeated 1 time(s)]
> surface #!1.2.6
Error processing trigger "setting changed":
"Nearby" atom/residue distance not valid
> view #!1.2.1 @< 3.5
> zoom 0.75
moved plane near -26.08374026050619 [ 0.56850353 0.34116689 -0.74860456]
moved plane far -26.08374026050619 [ 0.56850353 0.34116689 -0.74860456]
> ~surface #1.2
> surface #!1.2.1
> view #!1.2.6 @< 3.5
> zoom 0.75
moved plane near -38.00988394260593 [ 0.56850353 0.34116689 -0.74860456]
moved plane far -38.00988394260593 [ 0.56850353 0.34116689 -0.74860456]
> ~surface #1.2
> surface #!1.2.6
> view #1
> view #!1.2.6 @< 3.5
> zoom 0.75
moved plane near -38.00988394260593 [ 0.56850353 0.34116689 -0.74860456]
moved plane far -38.00988394260593 [ 0.56850353 0.34116689 -0.74860456]
> hide sel cartoons
> select clear
> select #!1/A:247@CG
1 atom, 1 residue, 1 model selected
> select #!1/A:398@OD2
1 atom, 1 residue, 1 model selected
> select #!1/A:276@CZ
1 atom, 1 residue, 1 model selected
> select #!1/A:247@CG
1 atom, 1 residue, 1 model selected
> select clear
> select #1.2.6/cavity:1@Z1367
1 atom, 1 residue, 1 model selected
> select up
2643 atoms, 1 residue, 2 models selected
> hide #* target a
> show (#!1.2.6 & sel) target ab
> select clear
> select #!1/A:425@NZ
1 atom, 1 residue, 1 model selected
> select #2/?:1@@serial_number=-1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/?:1@@serial_number=-1
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #!1/A:425@CE
1 atom, 1 residue, 1 model selected
> select #!1/A:198@NH2
1 atom, 1 residue, 1 model selected
> select #2/?:1@@serial_number=-1
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel surfaces
[Repeated 1 time(s)]
> select #!1/A:425@NZ
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #1.2.6/cavity:1@Z899
1 atom, 1 residue, 1 model selected
> select up
2643 atoms, 1 residue, 2 models selected
> surface hidePatches (#!1.2.6 & sel)
> undo
[Repeated 8 time(s)]
> select #!1/A:425@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
34 atoms, 33 bonds, 4 residues, 2 models selected
> select up
3301 atoms, 3356 bonds, 443 residues, 2 models selected
> select up
3301 atoms, 3356 bonds, 443 residues, 3 models selected
> select up
3301 atoms, 3356 bonds, 443 residues, 3 models selected
> hide sel surfaces
> select #1.2.6/cavity:1@Z1666
1 atom, 1 residue, 1 model selected
> select #1.2.6/cavity:1@Z1666
1 atom, 1 residue, 1 model selected
> select up
2643 atoms, 1 residue, 1 model selected
> show sel surfaces
> style sel sphere
Changed 2643 atom styles
> style sel sphere
Changed 2643 atom styles
> style sel sphere
Changed 2643 atom styles
> style sel ball
Changed 2643 atom styles
> style sel stick
Changed 2643 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> hide sel cartoons
> hide sel atoms
> show sel surfaces
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style image
No volumes specified
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> surface style #!1.2.6.1 mesh
> select clear
> ui tool show ViewDockX
No suitable models found for ViewDockX
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/mu_gpj/vina_dock.pdbqt
Summary of feedback from opening
/home/daniel/unicamp/EPSPS/autodock/GPJ/mu_gpj/vina_dock.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.102 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -5.258
Ignored bad PDB record found on line 4
REMARK INTER: -5.061
Ignored bad PDB record found on line 5
REMARK INTRA: -0.197
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.197
395 messages similar to the above omitted
Opened vina_dock.pdbqt containing 20 structures (240 atoms, 220 bonds)
> viewdockx #24.1-20
> hide #24.1-20 models
> show #24.1 models
> ui mousemode right rotate
> select #1.2.6/cavity:1@Z818
1 atom, 1 residue, 1 model selected
> select up
2643 atoms, 1 residue, 2 models selected
> select down
1 atom, 1 residue, 2 models selected
> select down
1 atom, 1 residue, 2 models selected
> hide #24.1 models
> show #24.1 models
> show #!2 target m
> hide #24.1 models
> show #24.1 models
> style sel ball
Changed 1 atom style
> select #1.2.6/cavity:1@Z1142
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #24.1 models
> show #24.2 models
> hide #24.2 models
> show #24.1 models
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select #1/A
3301 atoms, 3356 bonds, 443 residues, 1 model selected
> select #1/A
3301 atoms, 3356 bonds, 443 residues, 1 model selected
> ui tool show "Selection Inspector"
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel ball
Changed 12 atom styles
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/mu_gpj/cavidade_mu_gpj.cxs
——— End of log from Thu Apr 24 18:35:35 2025 ———
opened ChimeraX session
QItemSelectionModel: Selecting when no model has been set will result in a no-
op.
[Repeated 2 time(s)]
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/mu_gpj/mu_gpj.x3d
> open /home/daniel/unicamp/EPSPS/autodock/pep/wt/pep_wt.x3d
> close session
> open /home/daniel/unicamp/EPSPS/autodock/pep/wt/pep_wt.x3d
[Repeated 1 time(s)]
> close session
> open /home/daniel/unicamp/EPSPS/ScEPSPS/chimera_mu.py
> close session
mu_model_06.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ScEPSPSm [more info...]
Chain information for mu_model_06.pdb #1
---
Chain | Description
A | No description available
executed chimera_mu.py
> open /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/gpj_wt.py
> close session
wt_model_06.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ScEPSPS [more info...]
Chain information for wt_model_06.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in wt_model_06.pdb #1
---
GPJ — (GPJ)
MES — (MES)
S3P — (S3P)
executed gpj_wt.py
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
88 atoms, 89 bonds, 12 residues, 1 model selected
> select add #1//chain_id='_':1@O5
2 pseudobonds, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #1-2 atoms
> hide #1-2 cartoons
> show #1-2 atoms
> hide #1-2 cartoons
> hide #1-2 surfaces
> hide #1-2 atoms
> show #1-2 atoms
> select #1/A
3302 atoms, 3358 bonds, 443 residues, 1 model selected
> hide sel atoms
> select #1//chain_id='_':2@C1
Nothing selected
> select add #1//chain_id='_':2@C1
Nothing selected
> select add #1//chain_id='_':2@C1
Nothing selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
16 atoms, 16 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Find Cavities"
> kvfinder #1
17 cavities found for wt_model_06.pdb #1
wt_model_06.pdb Cavities
---
ID | | Volume | Area | Points
1.1.6 | | 548.86 | 564.92 | 2541
1.1.1 | | 131.98 | 132.78 | 611
1.1.4 | | 82.08 | 99.24 | 380
1.1.11 | | 53.35 | 73.2 | 247
1.1.12 | | 41.04 | 61.11 | 190
1.1.2 | | 38.66 | 54.64 | 179
1.1.15 | | 38.02 | 55.49 | 176
1.1.3 | | 27 | 49.65 | 125
1.1.8 | | 26.35 | 44.11 | 122
1.1.5 | | 24.84 | 34.1 | 115
1.1.17 | | 19.01 | 28.29 | 88
1.1.13 | | 12.31 | 29.54 | 57
1.1.16 | | 12.31 | 29.54 | 57
1.1.14 | | 11.45 | 19.17 | 53
1.1.10 | | 11.23 | 21.93 | 52
1.1.7 | | 9.29 | 16.65 | 43
1.1.9 | | 6.48 | 12.8 | 30
> view #1.1.6 @< 3.5
> zoom 0.75
moved plane near -23.87475993954258 [ 0.96270131 -0.22314441 -0.15301224]
moved plane far -23.87475993954258 [ 0.96270131 -0.22314441 -0.15301224]
> surface #1.1
> transparency #1.1 50
> ~surface #1.1
> surface #1.1.6
> view #!1.1.9 @< 3.5
> zoom 0.75
moved plane near -4.475905551570165 [ 0.00327389 -0.74011227 -0.67247535]
moved plane far -4.475905551570165 [ 0.00327389 -0.74011227 -0.67247535]
> ~surface #1.1
> surface #!1.1.9
> view #!1.1.6 @< 3.5
> zoom 0.75
moved plane near -23.84104540571936 [ 0.00327389 -0.74011227 -0.67247535]
moved plane far -23.84104540571936 [ 0.00327389 -0.74011227 -0.67247535]
> ~surface #1.1
> surface #!1.1.6
> view #!1.1.1 @< 3.5
> zoom 0.75
moved plane near -15.271511422043238 [ 0.00327389 -0.74011227 -0.67247535]
moved plane far -15.271511422043238 [ 0.00327389 -0.74011227 -0.67247535]
> ~surface #1.1
> surface #!1.1.1
> view #!1.1.6 @< 3.5
> zoom 0.75
moved plane near -23.84104540571936 [ 0.00327389 -0.74011227 -0.67247535]
moved plane far -23.84104540571936 [ 0.00327389 -0.74011227 -0.67247535]
> ~surface #1.1
> surface #!1.1.6
> ~surface #1.1
[Repeated 1 time(s)]
> surface #!1.1.6
> ui windowfill toggle
> select #1.1.6/cavity:1@Z1668
1 atom, 1 residue, 1 model selected
> select up
2541 atoms, 1 residue, 2 models selected
> show sel surfaces
> select ~sel & ##selected
Nothing selected
> hide #2#!1#!1.1.1-17 surfaces
> undo
[Repeated 1 time(s)]
> show sel surfaces
> surface style #1.1.6 mesh
> select ~sel
6067 atoms, 3578 bonds, 594 pseudobonds, 479 residues, 40 models selected
> select add #1.1.6/cavity:1@Z1185
6068 atoms, 3578 bonds, 594 pseudobonds, 480 residues, 57 models selected
> select subtract #1.1.6/cavity:1@Z1185
6067 atoms, 3578 bonds, 594 pseudobonds, 479 residues, 57 models selected
> select add #1.1.6/cavity:1@Z1185
6068 atoms, 3578 bonds, 594 pseudobonds, 480 residues, 57 models selected
> select add #1.1.6/cavity:1@Z774
6069 atoms, 3578 bonds, 594 pseudobonds, 480 residues, 58 models selected
> select subtract #1.1.6/cavity:1@Z774
6068 atoms, 3578 bonds, 594 pseudobonds, 480 residues, 58 models selected
> select clear
> select #1.1.4/cavity:1@Z329
1 atom, 1 residue, 1 model selected
> select up
380 atoms, 1 residue, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
> hide sel atoms
> select up
380 atoms, 1 residue, 2 models selected
> select up
5066 atoms, 17 residues, 18 models selected
> select down
380 atoms, 1 residue, 18 models selected
> ui mousemode right select
> ui mousemode right zone
[Repeated 5 time(s)]Drag select of 774 atoms
> hide sel atoms
Drag select of 5 atoms
Drag select of 28 atoms
Drag select of 149 atoms
> hide sel atoms
Drag select of 168 atoms
> hide sel atoms
Drag select of 226 atoms
> hide sel cartoons
> hide sel atoms
Drag select of 57 atoms
Drag select of 30 atoms
Drag select of 78 atoms
> hide sel atoms
Drag select of 327 atoms
Drag select of 3 atoms
[Repeated 1 time(s)]
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 11 atoms
Drag select of 57 atoms
> hide sel atoms
> select #1.1.6/cavity:1@Z2369
1 atom, 1 residue, 1 model selected
> select up
2541 atoms, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #1.1.6/cavity:1@Z1734
1 atom, 1 residue, 1 model selected
> select add #1.1.6/cavity:1@Z2072
2 atoms, 1 residue, 2 models selected
> select add #1.1.6/cavity:1@Z1909
3 atoms, 1 residue, 2 models selected
> select add #2/?:1@@serial_number=-1
15 atoms, 11 bonds, 2 residues, 3 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel ball
Changed 12 atom styles
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
Drag select of 179 atoms
> hide sel atoms
> undo
> select clear
Drag select of 179 atoms
> hide sel atoms
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
——— End of log from Thu Apr 24 18:54:12 2025 ———
opened ChimeraX session
> select #1.1.6/cavity:1@Z374
1 atom, 1 residue, 1 model selected
> select #1.1.6/cavity:1@Z1637
1 atom, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #!1/A
Alignment identifier is 1/A
> select /A:173
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> cartoon sel
> surface sel
> label (#!1 & sel) attribute name
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> hide sel atoms
> hide sel cartoons
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> view sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> show sel surfaces
> hide sel atoms
> hide sel cartoons
> select down
2 atoms, 1 bond, 1 residue, 2 models selected
> select down
1 bond, 2 models selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #3 models
> show #4 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> hide #17 models
> show #18 models
> show #17 models
> show #19 models
> show #20 models
> show #21 models
> hide #21 models
> hide #20 models
> hide #3-21 target m
> select ::name="PRO"
161 atoms, 164 bonds, 23 residues, 1 model selected
> select ::name="PRO"
161 atoms, 164 bonds, 23 residues, 1 model selected
> select ::name="UNL"
240 atoms, 220 bonds, 20 residues, 20 models selected
> select add #1.1.6.1.2
240 atoms, 220 bonds, 20 residues, 21 models selected
> select subtract #2
228 atoms, 209 bonds, 19 residues, 20 models selected
> select add #1
8596 atoms, 3567 bonds, 479 residues, 41 models selected
> select add #2
8608 atoms, 3578 bonds, 480 residues, 60 models selected
> select subtract #3
8596 atoms, 3567 bonds, 479 residues, 59 models selected
> select subtract #4
8584 atoms, 3556 bonds, 478 residues, 58 models selected
> select subtract #5
8572 atoms, 3545 bonds, 477 residues, 57 models selected
> select subtract #15
8560 atoms, 3534 bonds, 476 residues, 56 models selected
> select subtract #14
8548 atoms, 3523 bonds, 475 residues, 55 models selected
> select subtract #13
8536 atoms, 3512 bonds, 474 residues, 54 models selected
> select subtract #11
8524 atoms, 3501 bonds, 473 residues, 53 models selected
> select subtract #10
8512 atoms, 3490 bonds, 472 residues, 52 models selected
> select subtract #9
8500 atoms, 3479 bonds, 471 residues, 51 models selected
> select subtract #8
8488 atoms, 3468 bonds, 470 residues, 50 models selected
> select subtract #12
8476 atoms, 3457 bonds, 469 residues, 49 models selected
> select subtract #16
8464 atoms, 3446 bonds, 468 residues, 48 models selected
> select subtract #17
8452 atoms, 3435 bonds, 467 residues, 47 models selected
> select subtract #18
8440 atoms, 3424 bonds, 466 residues, 46 models selected
> select subtract #19
8428 atoms, 3413 bonds, 465 residues, 45 models selected
> select subtract #20
8416 atoms, 3402 bonds, 464 residues, 44 models selected
> select subtract #21
8404 atoms, 3391 bonds, 463 residues, 43 models selected
> select #1.1.6.1.2
1 model selected
> surface style #1.1.6.1.2 mesh
> select add #1.1.6/cavity:1@Z512
1 atom, 1 residue, 2 models selected
> select add #1
8368 atoms, 3358 bonds, 460 residues, 23 models selected
> select subtract #1
18 models selected
> select add #1.1
5066 atoms, 17 residues, 20 models selected
> select add #1.2
8368 atoms, 460 residues, 38 models selected
> surface style mesh
> select clear
Drag select of 32 atoms
> delete atoms (#!1.1.17 & sel)
> delete bonds (#!1.1.17 & sel)
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
> select #!1/A:173@O
1 atom, 1 residue, 1 model selected
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> color (#!1 & sel) yellow
> select /A:173
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select clear
> select /A:173
7 atoms, 7 bonds, 1 residue, 1 model selected
> surface style #1.2 dot
> surface style #1.2 mesh
> select clear
> hide #1.2 models
> show #1.2 models
> hide #!1.1 models
> show #!1.1 models
> select add #1.2
3302 atoms, 443 residues, 1 model selected
> color (#!1 & sel) light gray
> color (#!1 & sel) yellow
> select clear
> hide #1.3 models
> show #1.3 models
> hide #1.2 models
> show #1.2 models
> hide #!1.1 models
> show #!1.1 models
> select add #1.1
5034 atoms, 17 residues, 18 models selected
> color (#!1.1.1-17 & sel) white
> select clear
> select add #1.1
5034 atoms, 17 residues, 18 models selected
> transparency (#!1.1.1-17 & sel) 40
> select clear
> select #2/?:1@@serial_number=-1
12 atoms, 11 bonds, 1 residue, 1 model selected
> view sel
> select /A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select clear
> select #!1/A:169@CG2
1 atom, 1 residue, 1 model selected
> select #!1/A:169@CB
1 atom, 1 residue, 1 model selected
> select #!1/A:169@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> transparency (#!1 & sel) 0
> select clear
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
Cannot save
'/home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs': [Errno
121] Remote I/O error:
'/home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs.26319.tmp'
> select clear
[Repeated 1 time(s)]
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
> select add #1.1
5034 atoms, 17 residues, 18 models selected
> select subtract #1.1
17 models selected
> select add #1
8336 atoms, 3358 bonds, 460 residues, 20 models selected
> select subtract #1
18 models selected
> select add #1.2
3302 atoms, 443 residues, 1 model selected
> select subtract #1.2
1 model selected
> select add #1.1.1
611 atoms, 1 residue, 1 model selected
> select subtract #1.1.1
1 model selected
> select add #1.1.1
611 atoms, 1 residue, 1 model selected
> select subtract #1.1.1
1 model selected
> select add #1.1.2
179 atoms, 1 residue, 1 model selected
> select subtract #1.1.2
1 model selected
> select add #1.1
5034 atoms, 17 residues, 18 models selected
> color (#!1.1.1-17 & sel) magenta
> select clear
> save /home/daniel/unicamp/EPSPS/autodock/GPJ/wt_gpj/wt_gpj_session.cxs
——— End of log from Thu Apr 24 19:51:41 2025 ———
opened ChimeraX session
> select #!1/A
3302 atoms, 3358 bonds, 443 residues, 1 model selected
> show sel cartoons
> lighting simple
> lighting soft
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> ui mousemode right select
> select clear
> select #!1/A:407
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
93 atoms, 94 bonds, 13 residues, 1 model selected
> select up
3302 atoms, 3358 bonds, 443 residues, 2 models selected
> ui mousemode right clip
[Repeated 2 time(s)]
> ui mousemode right "clip rotate"
[Repeated 2 time(s)]
> ui mousemode right clip
Drag select of 7 residues
> select clear
> select #!1/A:176
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 14 residues, 2 models selected
> select up
3302 atoms, 3358 bonds, 443 residues, 2 models selected
> ui tool show AlphaFold
> alphafold match #1
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold A0A811SS62 from
https://alphafold.ebi.ac.uk/files/AF-A0A811SS62-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A811SS62 (chain
A)
AlphaFold prediction matching wt_model_06.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A811SS62 | A0A811SS62_9POAL | 0.93 | 443 | 443 | 100
Opened 1 AlphaFold model
> alphafold match #1
1 AlphaFold model found using sequence similarity searches: A0A811SS62 (chain
A)
AlphaFold prediction matching wt_model_06.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A811SS62 | A0A811SS62_9POAL | 0.93 | 443 | 443 | 100
Opened 1 AlphaFold model
> select clear
> close session
> open /home/daniel/unicamp/EPSPS/autodock/TIPS/epsps_tips.pdb
epsps_tips.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) TIPS [more info...]
Chain information for epsps_tips.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in epsps_tips.pdb #1
---
MES — (MES)
Computing secondary structure
> open /home/daniel/unicamp/EPSPS/autodock/TIPS/TIPS_pep/result.dock4
Unrecognized file suffix '.dock4'
> open /home/daniel/unicamp/EPSPS/autodock/TIPS/TIPS_pep/vina_dock.pdbqt
Summary of feedback from opening
/home/daniel/unicamp/EPSPS/autodock/TIPS/TIPS_pep/vina_dock.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -4.042 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -4.588
Ignored bad PDB record found on line 4
REMARK INTER: -4.751
Ignored bad PDB record found on line 5
REMARK INTRA: 0.163
Ignored bad PDB record found on line 6
REMARK UNBOUND: 0.163
355 messages similar to the above omitted
Opened vina_dock.pdbqt containing 20 structures (200 atoms, 180 bonds)
> viewdockx #2.1-20
> hide #2.1-20 models
> show #2.1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel ball
Changed 10 atom styles
Must select a number of stars next to the 'Close' button
> select clear
> ui tool show "Find Cavities"
No structures chosen
> select add #1/A:436
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 97 bonds, 12 residues, 1 model selected
> select up
3302 atoms, 3357 bonds, 443 residues, 1 model selected
> select up
3314 atoms, 3369 bonds, 444 residues, 1 model selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select down
3314 atoms, 3369 bonds, 444 residues, 1 model selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select up
3314 atoms, 3369 bonds, 444 residues, 2 models selected
> select add #2.1/?:1@P
3315 atoms, 3369 bonds, 445 residues, 3 models selected
> select up
3324 atoms, 3378 bonds, 445 residues, 3 models selected
> select up
3514 atoms, 3549 bonds, 464 residues, 22 models selected
> select up
3514 atoms, 3549 bonds, 464 residues, 22 models selected
> ui tool show "Find Cavities"
No structures chosen
> ui tool show "Find Cavities"
> kvfinder #1
17 cavities found for epsps_tips.pdb #1
epsps_tips.pdb Cavities
---
ID | | Volume | Area | Points
1.1.6 | | 554.9 | 587.93 | 2569
1.1.1 | | 131.98 | 132.78 | 611
1.1.4 | | 82.08 | 99.24 | 380
1.1.11 | | 53.35 | 73.2 | 247
1.1.12 | | 41.04 | 61.11 | 190
1.1.2 | | 38.66 | 54.64 | 179
1.1.15 | | 36.72 | 55.37 | 170
1.1.3 | | 30.02 | 53.54 | 139
1.1.8 | | 26.35 | 44.11 | 122
1.1.5 | | 24.84 | 34.1 | 115
1.1.17 | | 19.01 | 28.29 | 88
1.1.13 | | 12.31 | 29.54 | 57
1.1.16 | | 12.31 | 29.54 | 57
1.1.14 | | 11.45 | 19.17 | 53
1.1.10 | | 11.23 | 21.93 | 52
1.1.7 | | 8.42 | 15.53 | 39
1.1.9 | | 6.48 | 12.8 | 30
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 51, in data
widget.color = val
^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/color_button.py", line 82, in set_color
rgba = color_to_numpy_rgba8(color)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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: 4.6 (Core Profile) Mesa 24.2.8-1ubuntu1~24.04.1
OpenGL renderer: AMD Radeon Vega 3 Graphics (radeonsi, raven2, LLVM 19.1.1, DRM 3.57, 6.8.0-58-generic)
OpenGL vendor: AMD
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Acer
Model: Swift SF314-41
OS: Linux Mint 22.1
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 AMD Ryzen 3 3200U with Radeon Vega Mobile Gfx
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 5.7Gi 4.1Gi 665Mi 171Mi 1.4Gi 1.6Gi
Swap: 4.7Gi 1.2Gi 3.4Gi
Graphics:
03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Picasso/Raven 2 [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15d8] (rev c4)
Subsystem: Acer Incorporated [ALI] Picasso/Raven 2 [Radeon Vega Series / Radeon Vega Mobile Series] [1025:1378]
Kernel driver in use: amdgpu
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-LinuxSupport: 1.0.1
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
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
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: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.36.0
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
pexpect: 4.9.0
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
ptyprocess: 0.7.0
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: 0.7.3
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
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
toml: 0.10.2
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
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → General Controls |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Error setting cavity color |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #16362