id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14749 Clipper: not compatible with ChimeraX 1.8 wolfram.seifert@… Tristan Croll "{{{ 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 """", line 1204, in _gcd_import File """", line 1176, in _find_and_load File """", line 1147, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", 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 __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 """", line 1204, in _gcd_import File """", line 1176, in _find_and_load File """", line 1147, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", 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 __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 """", line 1204, in _gcd_import File """", line 1176, in _find_and_load File """", line 1147, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", 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 __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 """", line 1204, in _gcd_import File """", line 1176, in _find_and_load File """", line 1147, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", 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 __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 """", line 1204, in _gcd_import File """", line 1176, in _find_and_load File """", line 1147, in _find_and_load_unlocked File """", line 690, in _load_unlocked File """", line 940, in exec_module File """", 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 __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 }}} " defect closed normal Third Party fixed Greg Couch all ChimeraX