Opened 20 months ago

Closed 19 months ago

#14749 closed defect (fixed)

Clipper: not compatible with ChimeraX 1.8

Reported by: wolfram.seifert@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403091657 (2024-03-09 16:57:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
errors | Bundle 'ChimeraX-Clipper' custom initialization failed  
Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warnings | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 32, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 30, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 952, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 813, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 859, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.2
(c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 952, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 813, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 859, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.2
(c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
UCSF ChimeraX version: 1.8.dev202403091657 (2024-03-09)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> dssp

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_alphafold_fitted.pdb

Chain information for TauA_alphafold_fitted.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> set bgColor white

> set bgColor #ffffff00

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_test.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_test.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-DNA_test.pdb
#3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> select add #3

12301 atoms, 12752 bonds, 3 pseudobonds, 1377 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #3

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> dssp

> show #!1 models

> hide #!3 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_test-coot-0.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_test-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-DNA_test-
coot-0.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> dssp

> hide #!1,4 atoms

> show #!1,4 cartoons

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #2 models

> dssp minLenstrand 2

Expected a structures specifier or a keyword  

> dssp minLenstran 2

Expected a structures specifier or a keyword  

> dssp minStrandLen 2

> show #!4 models

> hide #2 models

> show #2 models

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_test-coot-0.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_test-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-DNA_test-
coot-0.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> dssp

> hide #2#!1,4-5 atoms

> show #2#!1,4-5 cartoons

> hide #!4 models

> hide #2 models

> hide #!1 models

> hide #!5 models

> show #!5 models

> show #2 models

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_test-coot-0.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_test-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-DNA_test-
coot-0.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> dssp

> hide #2#!5-6 atoms

> show #2#!5-6 cartoons

> hide #!5 models

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_test-coot-0.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_test-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-DNA_test-
coot-0.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> dssp

> hide #2#!6-7 atoms

> show #2#!6-7 cartoons

> hide #!6 models

> hide #!7 models

> color #2 bychain

> hide #2 models

> show #!7 models

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_fixing.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_fixing.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_fixing.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> dssp

> hide #!7-8 atoms

> show #!7-8 cartoons

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/job116_related_to_job103_local_resolution.mrc

Opened job116_related_to_job103_local_resolution.mrc as #9, grid size
320,320,320, pixel 0.822, shown at level 0.00246, step 2, values float32  

> transparency 60

> volume #9 step 1

> volume #9 level 0.004034

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> volume #9 level 0.007349

> show #!7 models

> hide #!7 models

> show #!8 atoms

> style #!8 stick

Changed 12301 atom styles  

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!1 models

> show #2 models

> hide #!1 models

> show #2 atoms

> close #8

> close

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
> DNA_fixing.pdb

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/Grzegorz_method/TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_fixing.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 S1 2 LEU A
232 ARG A 234 -1  
Start residue of secondary structure not found: SHEET 1 S610 THR A 263 LYS A
265 0  
Start residue of secondary structure not found: SHEET 3 S610 0 0 0  
Start residue of secondary structure not found: SHEET 4 S610 0 0 0  
Start residue of secondary structure not found: SHEET 5 S610 0 0 0  
5 messages similar to the above omitted  
  
Chain information for
TauA_coot_Isolde_ready_for_refinement1_DNA_shifted-3_poliA_poliT-
DNA_fixing.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> open
> C:/Users/wseif/Desktop/Cryosparc/Merge_datasets_RELION5/TauA/Refinement/job116_related_to_job103_local_resolution.mrc

Opened job116_related_to_job103_local_resolution.mrc as #2, grid size
320,320,320, pixel 0.822, shown at level 0.00246, step 2, values float32  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 32, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 30, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 952, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 813, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 859, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.2
(c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 329, in _register_cmd  
api = self._get_api(logger)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2223, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2154, in call  
return self.proxy()  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
clipper in bundle ChimeraX-Clipper:  
Error importing bundle ChimeraX-Clipper's module: (ChimeraX-AtomicLibrary
14.0.2 (c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2839, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2575, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2225, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'clipper' failed
(register_command() failed for command clipper in bundle ChimeraX-Clipper:  
Error importing bundle ChimeraX-Clipper's module: (ChimeraX-AtomicLibrary
14.0.2 (c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper'}))  
  
RuntimeError: delayed command registration for 'clipper' failed
(register_command() failed for command clipper in bundle ChimeraX-Clipper:  
Error importing bundle ChimeraX-Clipper's module: (ChimeraX-AtomicLibrary
14.0.2 (c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper'}))  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2225, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 952, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 813, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 859, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.2
(c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 396, in run_provider  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\wseif\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 952, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 813, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 859, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 14.0.2
(c:\program files\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper',
'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 396, in run_provider  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 14.0.2 (c:\program
files\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper', 'ChimeraX-ISOLDE'})  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 532.09
OpenGL renderer: NVIDIA GeForce RTX 2070 Super/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_DE.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: Alienware
Model: Alienware m15 R3
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,929,841,152
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.54.6
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    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: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403091657
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.2.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.36.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.8
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.49.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.3
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.8.2
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.1.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.42.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 20 months ago

Cc: Greg Couch added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper: not compatible with ChimeraX 1.8

comment:2 by Tristan Croll, 20 months ago

Oh, man... I messed up the "~=" version specifier in the dependencies section for both Clipper and ISOLDE (did ~=1.7, not ~=1.7.0). I was using the more specific ">=1.6.0,<1.7" version specifier in the previous build, but that ran into its own problems because 1.7.dev... is defined as less than 1.7. Sorry about that... anyway, the upshot is that it's *not* expected to be compatible with ChimeraX 1.8.x. Guess I'd better get some new builds out as soon as I get back from travelling.

comment:3 by Tristan Croll, 19 months ago

Resolution: → fixed
Status: assigned → closed

OK, fixed for now (uploaded new Clipper/ISOLDE builds, requiring yesterday's ChimeraX daily build or later). This will still come back to bite me once ChimeraX 1.9 rolls around... at that point the best course of action might be to remove the offending versions from the ToolShed.

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