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Opened 8 months ago
Closed 8 months ago
#17175 closed defect (duplicate)
Similar Structures: 'NoneType' object has no attribute 'hits'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
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
> "C:\\\Users\\\jiang\\\Desktop\\\TAAR348\\\structure\\\TAAR348_spermine_model\\\TAAR348_pocket
> interaction.cxs"
Log from Tue Mar 11 15:52:08 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/jiang/Desktop/interface.cxs
Log from Tue Mar 11 14:31:07 2025 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\\\jiang\\\Desktop\\\TAAR348\\\structure\\\TAAR348_spermine_model\\\TAAR348-coot-12.pdb
Chain information for TAAR348-coot-12.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
S | No description available
> set bgColor white
> hide atoms
> select /R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> color #1 #7096ffff
> ribbon style width 1.3 thick 0.3
> select clear
> select ::name="SPE"
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> save C:/Users/jiang/Desktop/interface.cxs includeMaps true
——— End of log from Tue Mar 11 14:31:07 2025 ———
opened ChimeraX session
> open
> C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/TAAR348-coot-12.pdb
Chain information for TAAR348-coot-12.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
N | No description available
R | No description available
S | No description available
> hide sel atoms
> select add #2
9832 atoms, 10040 bonds, 3 pseudobonds, 1272 residues, 3 models selected
> select add #1
19636 atoms, 20054 bonds, 6 pseudobonds, 2542 residues, 4 models selected
> hide #!1 models
> select subtract #1
9818 atoms, 10027 bonds, 3 pseudobonds, 1271 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> show #!1 models
> select add #1
12041 atoms, 12303 bonds, 4 pseudobonds, 1557 residues, 4 models selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select clear
> hide cartoons
> select #1/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select add #1
12041 atoms, 12303 bonds, 4 pseudobonds, 1557 residues, 4 models selected
> select add #2
19636 atoms, 20054 bonds, 6 pseudobonds, 2542 residues, 4 models selected
> select clear
> color #2 #7096ffff
> select add #1
9818 atoms, 10027 bonds, 3 pseudobonds, 1271 residues, 2 models selected
> select add #2
19636 atoms, 20054 bonds, 6 pseudobonds, 2542 residues, 4 models selected
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> ui windowfill toggle
[Repeated 1 time(s)]
> ribbon style width 1.3 thick 0.3
> select clear
> select ::name="SPE"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> color (#!2 & sel) yellow
> color (#!2 & sel) byhetero
> select sel :< 5
322 atoms, 316 bonds, 34 residues, 2 models selected
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 161 atom styles
> color (#!2 & sel) byhetero
> hide sel & #!2 atoms
> show sel & #!2 atoms
> hide sel & #!2 cartoons
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> color #1 #7096ff50
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 atoms
> hide #!2 models
> show #!2 models
> show #!2 atoms
> style #!2 stick
Changed 9818 atom styles
> hide #!2 atoms
> hide #!2 cartoons
> select #2/N
964 atoms, 986 bonds, 127 residues, 1 model selected
> show sel cartoons
> color #2 #7096ffff
> show sel cartoons
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select add #2
9818 atoms, 10027 bonds, 3 pseudobonds, 1271 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select add #2
9818 atoms, 10027 bonds, 3 pseudobonds, 1271 residues, 2 models selected
> select ::name="SPE"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> color (#!2 & sel) yellow
> color (#!2 & sel) byhetero
> select sel :< 5
322 atoms, 316 bonds, 34 residues, 2 models selected
> show sel & #!2 atoms
> color (#!2 & sel) byhetero
> select clear
> hide #!2 cartoons
> show #!1 models
> hide #!1 models
> show #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> show #!2 surfaces
> hide #!2 surfaces
> hide mainchain
> hide #!2 models
> show #!2 models
> hide #!2 cartoons
> show #!1 models
> hide #!1 models
> select add #1
9818 atoms, 10027 bonds, 3 pseudobonds, 1271 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
9818 atoms, 10027 bonds, 3 pseudobonds, 1271 residues, 2 models selected
> show sidechain
> hide sel atoms
> select ::name="SPE"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 cartoons
> show sel & #!2 atoms
> select clear
> show sel cartoons
[Repeated 1 time(s)]
> select clear
> show #!2 cartoons
> select clear
> hide #!2 cartoons
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select clear
> select #2/R:401@C06
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
2223 atoms, 2276 bonds, 286 residues, 1 model selected
> select clear
> select #2/R:401@C06
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> select sel :< 5
322 atoms, 316 bonds, 34 residues, 2 models selected
> show sel & #!2 atoms
> show sidechain
> hide sidechain
> show sel sidechain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sidechain
> hide sidechain
> name frozen sel sel
"sel" is reserved and cannot be redefined
> name frozen sel3 sel
> show sidechain
> show 3 sidechain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #3 sidechain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel & #!2 atoms
> select clear
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> hide #!2 atoms
> show #!2 atoms
> hide #!2 atoms
> show #!2 cartoons
> hide #!2 cartoons
> undo
[Repeated 4 time(s)]
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select clear
> graphics silhouettes true
> lighting shadows false
> lighting flat
> show #!1 models
> select #2/R:297@OH
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select #2/R:401@C10
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 2 models selected
> select add #2/R:112@CG
29 atoms, 28 bonds, 3 residues, 2 models selected
> select up
36 atoms, 35 bonds, 3 residues, 2 models selected
> view sel
> select clear
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting flat
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting flat
> hide cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1 #770099ff
> color #1 #7096ffff
> color #1 #7096ff50
> select #1/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select clear
> hide #!1 models
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> show sel cartoons
> select clear
> select #2/R:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
198 atoms, 203 bonds, 26 residues, 2 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show "Side View"
> select #2/R:206
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/R
2223 atoms, 2276 bonds, 1 pseudobond, 286 residues, 2 models selected
> color (#!2 & sel) #ffffffff
> color (#!2 & sel) #770099ff
> color (#!2 & sel) #7096ffff
> color (#!2 & sel) #7096ff02
> color (#!2 & sel) #7096ff14
> color (#!2 & sel) #7096ffc8
> select clear
> undo
[Repeated 7 time(s)]
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> select sel :< 5
322 atoms, 316 bonds, 34 residues, 2 models selected
> ui tool show "Render/Select by Attribute"
No attribute chosen for rendering
> volume appearance brain
No volumes specified
> volume appearance airways
No volumes specified
> volume projectionMode 2d-xyz
No volumes specified
> ui mousemode right "mark center"
> ui mousemode right "mark surface"
> ui mousemode right "mark plane"
> ui mousemode right "mark maximum"
> ui mousemode right "mark center"
> select clear
> save "C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/pocket
> interaction.png" width 3000 height 1785 supersample 4 transparentBackground
> true
> save
> "C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/TAAR348_pocket
> interaction.cxs" includeMaps true
——— End of log from Tue Mar 11 15:52:08 2025 ———
opened ChimeraX session
> hide #!2 atoms
> select ::name="SPE"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R #2/R
Alignment identifier is 1
> select #1/R:277 #2/R:277
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/R:277 #2/R:277
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [239] RMSD: 0.000
> select #1/R:277,289 #2/R:277,289
46 atoms, 46 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [239] + 1 other block RMSD: 0.000
> show sel & #!2 atoms
> select clear
> save "C:/Users/jiang/Desktop/EW motif.cxs" includeMaps true
> select add #2/R:277@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
> hbonds angleSlop 40.0 reveal true
5036 hydrogen bonds found
> ui tool show Foldseek
> ui tool show H-Bonds
> hbonds reveal true
4112 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel showDist true reveal true
6 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel reveal true
6 hydrogen bonds found
> select clear
[Repeated 1 time(s)]No visible atoms, bonds, or surfaces selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
Restriction atom specifier must not be blank
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select add #2/R:277@CD
15 atoms, 15 bonds, 2 residues, 2 models selected
> select up
23 atoms, 23 bonds, 2 residues, 2 models selected
> ui tool show H-Bonds
Restriction atom specifier must not be blank
> select clear
Drag select of 1 pseudobonds
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 atoms
> show #!2 atoms
> hide #!2 atoms
> ~hbonds
> select ::name="SPE"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> select #1/R:277 #2/R:277
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/R:277 #2/R:277
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [239] RMSD: 0.000
> select #1/R:277,289 #2/R:277,289
46 atoms, 46 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [239] + 1 other block RMSD: 0.000
> show sel & #!2 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
> hbonds sel reveal true
6 hydrogen bonds found
> select clear
[Repeated 1 time(s)]
> delete pseudobonds sel
> hbonds #!2 reveal true
3084 hydrogen bonds found
> ~hbonds
> select #2/R:277@OE2
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true
Atom specifier selects no atoms
> ui tool show H-Bonds
> hbonds sel reveal true
Atom specifier selects no atoms
> select clear
> select #2/R:401@C08
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel saltOnly true reveal true
4 hydrogen bonds found
> select #2/R:277@CD
1 atom, 1 residue, 1 model selected
> select clear
> ~hbonds
> select #2/R:277@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
> hbonds sel saltOnly true reveal true
2 hydrogen bonds found
> select #2/R:289@NE1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> hbonds sel reveal true
4 hydrogen bonds found
> ~hbonds
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hbonds sel reveal true
6 hydrogen bonds found
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> ~hbonds
> ui mousemode right distance
> select #2/R:277@OE2
1 atom, 1 residue, 1 model selected
> select #2/R:401@N04
1 atom, 1 residue, 1 model selected
> select add #2/R:277@OE2
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
[Repeated 1 time(s)]
> ui mousemode right translate
> select clear
> select #2/R:277@OE2
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/R:277@OE2
1 atom, 1 residue, 1 model selected
> select #2/R:401@N04
1 atom, 1 residue, 1 model selected
> select clear
> select #2/R:277@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hbonds sel reveal true
6 hydrogen bonds found
> select clear
> delete pseudobonds sel
> ui mousemode right select
> select clear
> delete pseudobonds sel
> ui tool show "Side View"
> hide #!2 atoms
> select ::name="SPE"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> select #1/R:277 #2/R:277
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/R:277 #2/R:277
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [239] RMSD: 0.000
> select #1/R:277,289 #2/R:277,289
46 atoms, 46 bonds, 2 pseudobonds, 4 residues, 3 models selected
1 [ID: 1] region 2 chains [239] + 1 other block RMSD: 0.000
> show sel & #!2 atoms
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> save "C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/EW
> motif.cxs" includeMaps true
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save
> C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/EWmotif.cxs
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save
> C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/EWmotif.png
> width 3000 height 2098 supersample 4 transparentBackground true
> save
> C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/EWmotif.cxs
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save C:/Users/jiang/Desktop/TAAR348/structure/TAAR348_spermine_model/EW.cxs
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save C:/Users/jiang/Desktop/EWmotif.cxs
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\tools.py", line 278, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x0000012BAA771CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000012BAA771CD0>
ValueError: error processing: 'tools' -> : Error while saving session data for
'tools' ->
File "D:\jiang\software\chimeraX\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: LENOVO
Model: 83DF
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 34,141,495,296
MaxProcessMemory: 137,438,953,344
CPU: 32 Intel(R) Core(TM) i9-14900HX
OSLanguage: zh-CN
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: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
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: 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
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
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
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 , 8 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Similar Structures: 'NoneType' object has no attribute 'hits' |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Fixed several months ago. Saving a session with Similar Structures tool shown but no search done.