![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7083 closed defect (can't reproduce)
Dead pseudobond group
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22000
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 "C:\Users\giuli\OneDrive\Documenti\PhD\MS
> project\analysis\ChimeraX_XMAS\LDb1_alphafold_XL.cxs" format session
Log from Thu Jun 9 18:17:35 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\giuli\Documents\chimeraSession_ldb1_alphafold.cxs format
> session
Log from Thu Jun 9 17:52:52 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\giuli\OneDrive\Documenti\PhD\MS
> project\analysis\ChimeraX_XMAS\SCLE47LMO2LDB1_2ypa\2ypa.cxs" format session
Log from Thu May 12 16:15:29 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 "C:/Users/giuli/OneDrive/Documenti/PhD/MS
> project/analysis/XlinkAnalyzer/scl-E47-LMO2-LDB1/2ypa.pdb"
2ypa.pdb title:
Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA [more info...]
Chain information for 2ypa.pdb #1
---
Chain | Description | UniProt
A | T-cell acute lymphocytic leukemia protein 1 | TAL1_HUMAN
B | transcription factor E2-α | TFE2_HUMAN
C | rhombotin-2 | RBTN2_HUMAN
D | lim domain-binding protein 1 | LDB1_HUMAN
E | ebox forward |
F | ebox reverse |
Non-standard residues in 2ypa.pdb #1
---
ZN — zinc ion
> style stick
Changed 2894 atom styles
> style stick
Changed 2894 atom styles
> show cartoons
> hide atoms
> open C:/Users/giuli/OneDrive/Desktop/SRCH=12477--ChimeraX--
> MAN.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.PEPLEN=1.PASS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-0.GROUPS=NA.DIST=0-35.pb
Opened Pseudobonds SRCH=12477--ChimeraX--
MAN.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.PEPLEN=1.PASS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-0.GROUPS=NA.DIST=0-35.pb,
5 bonds
> ui tool show XMAS
> save "C:/Users/giuli/OneDrive/Documenti/PhD/MS
> project/analysis/ChimeraX_XMAS/2ypa/2ypa_XL.pb" #2
Saved 5 pseudobonds to file C:/Users/giuli/OneDrive/Documenti/PhD/MS
project/analysis/ChimeraX_XMAS/2ypa/2ypa_XL.pb
C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:1100: UserWarning: Tight layout not applied.
The left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
Venn diagrams can only be plotted for two or three groups
Venn diagrams can only be plotted for two or three groups
Venn diagrams can only be plotted for two or three groups
C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:1100: UserWarning: Tight layout not applied.
The left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
> save "C:/Users/giuli/OneDrive/Documenti/PhD/MS
> project/analysis/ChimeraX_XMAS/SCLE47LMO2LDB1_2ypa/2ypa.cxs"
——— End of log from Thu May 12 16:15:29 2022 ———
opened ChimeraX session
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 1032, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 680, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 535, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 588, in reset_state
for pbg in list(self.group_map.values()):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> open "C:\Users\giuli\OneDrive\Documenti\PhD\MS
> project\analysis\AlphaFoldLdb1.pdb" format pdb
AlphaFoldLdb1.pdb title:
Alphafold V2.0 prediction for lim domain-binding protein 1 (P70662) [more
info...]
Chain information for AlphaFoldLdb1.pdb #1
---
Chain | Description | UniProt
A | lim domain-binding protein 1 | LDB1_MOUSE
Alignment identifier is 1/A
> label chain display
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> select 1-55
Expected an objects specifier or a keyword
> select
> /A:2-6,103-110,113-120,136-144,147-150,154-159,161-168,175-187,196-207
593 atoms, 599 bonds, 73 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-82
644 atoms, 669 bonds, 82 residues, 1 model selected
> select
> /A:2-6,103-110,113-120,136-144,147-150,154-159,161-168,175-187,196-207
593 atoms, 599 bonds, 73 residues, 1 model selected
> select /A:66-80,87-97,121-123,125-132,210-215,220-226,237-262,266-282
810 atoms, 823 bonds, 93 residues, 1 model selected
> select /A:1-82
644 atoms, 669 bonds, 82 residues, 1 model selected
> ui tool show "Command Line Interface"
> ui tool show "Build Structure"
> color sel red
> select aa 1:200
Expected an objects specifier or a keyword
> ui mousemode right "link markers"
[Repeated 1 time(s)]
> select
3258 atoms, 3344 bonds, 411 residues, 1 model selected
> select down
3258 atoms, 3344 bonds, 411 residues, 1 model selected
> select chain A
Expected an objects specifier or a keyword
> select : chain A
Expected a keyword
> select :/isHelix
Expected an objects specifier or a keyword
> select none
Expected an objects specifier or a keyword
> select #:1-200
Expected an objects specifier or a keyword
> select :1-200
1629 atoms, 1685 bonds, 200 residues, 1 model selected
> select :1-237
1926 atoms, 1986 bonds, 237 residues, 1 model selected
> color sel cornflower blue
> toolshed show
> $ label @@display
Unknown command: $ label @@display
> $label
Unknown command: $label
> $ label
Unknown command: $ label
> label @@display
[Repeated 1 time(s)]
> ui tool show "Model Panel"
> view clip false
> ui mousemode right label
[Repeated 2 time(s)]
> label delete
> label @@display
> 2dlabels
> 2dlabels selection
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels text "self-association domain"
> 2dlabels text "self-association domain" color light seagreen
> select #2.1
1 model selected
> ~select #2.1
Nothing selected
> select #2.1
1 model selected
> ~select #2.1
Nothing selected
> select #2.1
1 model selected
> 2dlabels delete
> 2dlabels text self-association' color cornflower blue
> label delete residues
> 2dlabels text self-association' color cornflower blue size 26 xpos .03 ypos
> .92
> select #3.1
1 model selected
> label delete residues
[Repeated 2 time(s)]
> 2dlabels labels delete
Invalid "labels" argument: Expected 'all' or a 2d label name or a label models
specifier
> 2dlabels delete
> 2dlabels text "self-association domain" color cornflower blue size 10 xpos
> 0.3 ypos .92
> 2dlabels text "self-association domain" color cornflower blue size 15 xpos
> 0.3 ypos .92
> 2dlabels text "self-association domain" color cornflower blue size 20 xpos
> 0.3 ypos .92
> 2dlabels text "self-association domain" color cornflower blue size 20 xpos
> 0.3 ypos .92: wait 60
Invalid "ypos" argument: Expected a number
> select #4
4 models selected
> ~select #4.1
3 models selected
> ~select #4.2
2 models selected
> ~select #4.3
1 model selected
> select #4.2
1 model selected
> select #4.1
1 model selected
> ~select #4.1
Nothing selected
> hide #4.1 models
> hide #4.2 models
> 2dlabels text "self-association domain" color cornflower blue size 20 xpos
> .03 ypos .92: wait 60
Invalid "ypos" argument: Expected a number
> 2dlabels text "self-association domain" color cornflower blue size 20 xpos
> .03 ypos .92
> hide #4.3 models
> select : 336-364
223 atoms, 224 bonds, 29 residues, 1 model selected
> color red
> color: selection red
Unknown command: color: selection red
> color sel magenta
> 2dlabels text "LID domain" magenta blue size 15 x .03 y .92
Expected a keyword
> hide #4.3 models
> 2dlabels text "self-association domain" color cornflower blue size 15 xpos
> .03 ypos .92
> hide #4.4 models
> 2dlabels text "LID domain" color magenta size 15 xpos .03 ypos .92
> hide #4.6 models
> show #4.6 models
> select #4.6
1 model selected
> label delete residues
[Repeated 2 time(s)]
> ui mousemode right "move picked models"
> ui mousemode right select
> ui mousemode right "move planes"
> log metadata #1
Metadata for AlphaFoldLdb1.pdb #1
---
Title | Alphafold V2.0 prediction for lim domain-binding protein 1 (P70662)
Source (natural) | Mus musculus
> log chains #1
Chain information for AlphaFoldLdb1.pdb #1
---
Chain | Description | UniProt
A | lim domain-binding protein 1 | LDB1_MOUSE
> log metadata #1
Metadata for AlphaFoldLdb1.pdb #1
---
Title | Alphafold V2.0 prediction for lim domain-binding protein 1 (P70662)
Source (natural) | Mus musculus
> log chains #1
Chain information for AlphaFoldLdb1.pdb #1
---
Chain | Description | UniProt
A | lim domain-binding protein 1 | LDB1_MOUSE
> log metadata #1
Metadata for AlphaFoldLdb1.pdb #1
---
Title | Alphafold V2.0 prediction for lim domain-binding protein 1 (P70662)
Source (natural) | Mus musculus
> log chains #1
Chain information for AlphaFoldLdb1.pdb #1
---
Chain | Description | UniProt
A | lim domain-binding protein 1 | LDB1_MOUSE
> view clip false
> select down
1 model selected
> select down
1 model selected
> select down
1 model selected
> select down
1 model selected
> select down
1 model selected
> hide #1 models
> ui mousemode right label
> ui mousemode right rotate
> ui tool show ViewDockX
No suitable models found for ViewDockX
> 2dlabels text "LID domain" color magenta size 15 xpos .04 ypos .92
> hide #4.7 models
> 2dlabels text "LID domain" color magenta size 15 xpos .03 ypos .82
> 2dlabels text "LID domain" color magenta size 15 xpos .03 ypos .90
> 2dlabels text "LID domain" color magenta size 15 xpos .03 ypos .88
> hide #4.8 models
> hide #4.9 models
> hide #4.6 models
> show #1 models
> select #4.5
1 model selected
> view #4.5 clip false
[Repeated 2 time(s)]
> hide #4.10 models
> show #4.10 models
> 2dlabels change 'self-association domain'
Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier
> 2dlabels change : 'self-association domain'
Expected a keyword
> 2dlabels change text 'self-association domain'
Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier
> 2dlabels change text 'self-association domain'
Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier
> 2dlabels text "self-association domain"
> hide #4.11 models
> 2dlabels change 'self-association domain'
Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier
> 2dlabels change self-association domain
Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier
> 2dlabels delete 'self-association domain'
Expected 'all' or a label/arrow models specifier or a keyword
> help help:user/tools/modelpanel.html
> 2dlabels delete 4.2
Expected 'all' or a label/arrow models specifier or a keyword
> 2dlabels delete #4.4
> 2dlabels delete #4.2
> 2dlabels delete #4.1
> 2dlabels delete #4.3
> 2dlabels delete #4.6
> 2dlabels delete #4.7
> 2dlabels delete #4.8
> 2dlabels delete #4.9
> 2dlabels delete #4.11
> 2dlabels change #4.5
> 2dlabels change #4.5 color blue
> 2dlabels change #4.5 color cornflower blue
> 2dlabels change #4.5 text "self-association & LIM-bind" color cornflower
> blue
> select : 336-375
306 atoms, 308 bonds, 40 residues, 1 model selected
> color sel magenta
> select #1
3258 atoms, 3344 bonds, 411 residues, 1 model selected
> ~select #1
Nothing selected
> select : 237-285
405 atoms, 414 bonds, 49 residues, 1 model selected
> color sel forest green
> 2dlabels text LCCD color forest green size 20 xpos .03 ypos .84
> 2dlabels text LCCD color forest green size 15 xpos .03 ypos .84
> 2dlabels delete #4.1
> label lys
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label atoms lys
Expected a keyword
> label: lys
Unknown command: label: lys
> label:lys
Unknown command: label:lys
> label : lys
> color sel byelement
> select : lys
189 atoms, 170 bonds, 21 residues, 1 model selected
> color sel yellow
> select #1
3258 atoms, 3344 bonds, 411 residues, 2 models selected
> ~select #1
Nothing selected
> 2dlabels text lysines color yellow size 15 xpos .03 ypos .80
> save C:/Users/giuli/Documents/chimeraSession_ldb1_alphafold.cxs
——— End of log from Thu Jun 9 17:52:52 2022 ———
opened ChimeraX session
> ui tool show XMAS
Please select pseudobonds
Traceback (most recent call last):
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc
return self._engine.get_loc(casted_key)
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'Score'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__
df = self.make_df(evidence_file, delimiter, header)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df
if (df[score_col].dtypes != "float64" and delimiter != ","):
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__
indexer = self.columns.get_loc(key)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: 'Score'
KeyError: 'Score'
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
Traceback (most recent call last):
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3621, in get_loc
return self._engine.get_loc(casted_key)
File "pandas\\_libs\index.pyx", line 136, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\index.pyx", line 163, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'Score'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 285, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 37, in __init__
evidence = cls(evidence_file)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 102, in __init__
df = self.make_df(evidence_file, delimiter, header)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\read_evidence.py", line 282, in make_df
if (df[score_col].dtypes != "float64" and delimiter != ","):
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\frame.py", line 3505, in __getitem__
indexer = self.columns.get_loc(key)
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: 'Score'
KeyError: 'Score'
File "C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\pandas\core\indexes\base.py", line 3623, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
> open "C:/Users/giuli/OneDrive/Documenti/PhD/MS
> project/analysis/ChimeraX_XMAS/SRCH=12477--ChimeraX--
> MAN.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.APART=0.PEPLEN=1.PASS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-0.GROUPS=NA.pb"
Opened Pseudobonds SRCH=12477--ChimeraX--
MAN.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.APART=0.PEPLEN=1.PASS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-0.GROUPS=NA.pb,
4 bonds
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
Venn diagrams can only be plotted for two or three groups
C:\Users\giuli\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:1100: UserWarning: Tight layout not applied.
The left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
Find shortest option unavailable for SRCH=12477--ChimeraX--
MAN.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.APART=0.PEPLEN=1.PASS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-0.GROUPS=NA.pb:
model has not been generated with XMAS
> deselect all
Unknown command: deselect all
> deselect
Unknown command: deselect
> ~select #2
Nothing selected
> save "C:/Users/giuli/OneDrive/Documenti/PhD/MS
> project/analysis/ChimeraX_XMAS/LDb1_alphafold_XL.cxs"
——— End of log from Thu Jun 9 18:17:35 2022 ———
opened ChimeraX session
> save "C:/Users/giuli/OneDrive/Documenti/PhD/MS
> project/analysis/ChimeraX_XMAS/LDb1_alphafold_XL2.cxs" includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 472.19
OpenGL renderer: NVIDIA GeForce MX450/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82NJ
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 16,487,870,464
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 9 5900HS Creator Edition
OSLanguage: en-US
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-XMAS: 1.1.1
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
et-xmlfile: 1.1.0
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openpyxl: 3.0.9
openvr: 1.16.801
packaging: 21.3
pandas: 1.4.2
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
seaborn: 0.11.2
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Dead pseudobond group |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
This will be a lot easier to debug in 1.4