id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19485 Crash in python_instances_of_class haniehbahrami@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000208bf9f00 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 52 in File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in python_instances_of_class File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 2642 in File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py"", line 290 in File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py"", line 290 in include_state File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 260 in discovery File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 646 in save File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 922 in save File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 307 in event_loop File 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: ""mmcif.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 12913868800, ""size"" : 409600, ""uuid"" : ""eec6c57b-e8da-3309-88a0-09dccfa5ed24"", ""path"" : ""\/Applications\/ChimeraX-1.8-rc2024.05.30.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so"", ""name"" : ""_mmcif.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5944508416, ""size"" : 81920, ""uuid"" : ""d7bd530c-3353-37a6-b81f-ee3179d65811"", ""path"" : ""\/Applications\/ChimeraX-1.8-rc2024.05.30.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so"", ""name"" : ""_version.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 6044123136, ""size"" : 180224, ""uuid"" : ""87eed069-25fc-30f6-aa30-1e54859d92e2"", ""path"" : 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""com.apple.main-thread"" } }, ""logWritingSignature"" : ""c1a73ca72bceae2ab2eb978a41f5b091cc7eafd2"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""6761d0c9df60af01adb250fb"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Errors --- error | Bundle 'ChimeraX-Clipper' custom initialization failed warning | Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 501, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 ""/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/clipper/__init__.py"", line 32, in __version__ = _version() ^^^^^^^^^^ File ""/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/clipper/__init__.py"", line 30, in _version return pkg_resources.require('ChimeraX-Clipper')[0].version ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/pkg_resources/__init__.py"", line 937, in require needed = self.resolve(parse_requirements(requirements)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/pkg_resources/__init__.py"", line 798, in resolve dist = self._resolve_dist( ^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/pkg_resources/__init__.py"", line 844, in _resolve_dist raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202405282004 (/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 375, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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-Core 1.8rc202405282004 (/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'}) UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/h.b/Downloads/sfgfpnB15_refine_042.pdb format pdb Chain information for sfgfpnB15_refine_042.pdb #1 --- Chain | Description A | No description available B E G | No description available C D F H | No description available > set bgColor white > graphics silhouettes true > show cartoons > hide atoms > select /g,h 2831 atoms, 2890 bonds, 363 residues, 1 model selected > delete ~sel > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /d Nothing selected > select /g 1857 atoms, 1900 bonds, 233 residues, 1 model selected > color sel green > ui tool show ""Color Actions"" > color sel yellow green > color sel lime > color sel spring green > color sel lime green > color sel medium sea green > color sel sea green > color sel spring green > ui tool show ""Color Actions"" > color sel #8eff8cff > color sel #7cff61ff > color sel #63ff3dff > color sel #67ff2eff > color sel #50ff2eff > color sel #47ff34ff > color sel #57ff47ff > color sel #2fff23ff > color sel #45ff3aff > color sel #41ff52ff > color sel #47ff7fff > color sel #36ff55ff > color sel #0cff67ff > color sel #09ff3bff > color sel #0eff1fff > color sel #3eff10ff > color sel #fff55aff > color sel #86ff65ff > color sel #77ff77ff > color sel #77ff76ff > color sel #8dff99ff > color sel #70ff8bff > color sel #61ff57ff > color sel #56ff64ff > color sel #3eff52ff > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /h 974 atoms, 990 bonds, 130 residues, 1 model selected > color sel plum > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /h 974 atoms, 990 bonds, 130 residues, 1 model selected > color sel hot pink > color sel #ffc7e6ff > color sel #e5b1ffff > color sel #e5b0ffff > color sel #ffabd4ff > color sel #ff6fb6ff > color sel #ff87cfff > color sel #ff8ce4ff > color sel #ff9efcff > color sel #ff96d6ff > color sel #ff5d7dff > color sel #ff74adff > color sel #ff89c6ff > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > save /Users/h.b/Desktop/gfpnB.png width 3000 height 2000 > transparentBackground true supersample 3 > select /h 974 atoms, 990 bonds, 130 residues, 1 model selected > select /g 1857 atoms, 1900 bonds, 233 residues, 1 model selected > color sel #ff89c6ff > color sel #a4ff9eff > color sel #8cff6cff > color sel #6cff39ff > color sel #57ff3aff > color sel #6dff1fff > color sel #53ff38ff > color sel #3cff3aff > color sel #4bff47ff > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > save /Users/h.b/Desktop/gfpnB.png width 3000 height 2000 > transparentBackground true supersample 3 > select /G:190 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /G:191 12 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > hide sel surfaces > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > show sel atoms > style sel stick Changed 2831 atom styles > hide sel atoms > select subtract #1 Nothing selected > select /G:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /H:55 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select /H:34 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select /H:56 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > undo > select subtract #1 Nothing selected > select /G:117@CD 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /G:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel byhetero > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /H:106 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /H:103 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /G:92 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /G:91 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select /G:90 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > color byhetero > select /H:103 11 atoms, 10 bonds, 1 residue, 1 model selected > select add /H:104 15 atoms, 13 bonds, 2 residues, 1 model selected > select add /H:105 26 atoms, 24 bonds, 3 residues, 1 model selected > select add /H:106 32 atoms, 29 bonds, 4 residues, 1 model selected > select add /H:107 39 atoms, 35 bonds, 5 residues, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /G:117 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /G:118 13 atoms, 11 bonds, 2 residues, 1 model selected > select add /G:119 21 atoms, 18 bonds, 3 residues, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /G:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /G:115 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /H:32 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /H:33 14 atoms, 12 bonds, 2 residues, 1 model selected > select add /H:34 20 atoms, 17 bonds, 3 residues, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /H:102 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /G:90@CG 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 2 residues, 1 model selected > select up 15 atoms, 15 bonds, 2 residues, 1 model selected > hide sel atoms > select /G:9 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select /G:119@OD2 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 12 atoms, 11 bonds, 2 residues, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select /H:34@CB 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /H:102@OG1 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 62 atoms, 62 bonds, 8 residues, 1 model selected > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > select /H:102@OG1 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected Drag select of 1 atoms, 15 residues > select add #1 2831 atoms, 2890 bonds, 363 residues, 1 model selected > select subtract #1 Nothing selected > ui tool show ""Side View"" > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > select /G:117@OE1 1 atom, 1 residue, 1 model selected > select add /H:56@OG1 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance /G:117@OE1 /H:56@OG1 Distance between /G GLU 117 OE1 and /H THR 56 OG1: 2.866Å > distance style decimalPlaces 2 > distance style decimalPlaces 1 > select add #1 2831 atoms, 2890 bonds, 1 pseudobond, 363 residues, 2 models selected > select subtract #1 Nothing selected > select /G:92@OE1 1 atom, 1 residue, 1 model selected > select add /H:103@NH1 2 atoms, 2 residues, 1 model selected > distance /G:92@OE1 /H:103@NH1 Distance between /G GLU 92 OE1 and /H ARG 103 NH1: 4.2Å > select add #1 2831 atoms, 2890 bonds, 2 pseudobonds, 363 residues, 2 models selected > select subtract #1 Nothing selected > distance style symbol false > hide #2.1 models > save /Users/h.b/Desktop/gfpnBclose.png width 3000 height 2000 > transparentBackground true supersample 3 > hide #!2 models Drag select of 24 atoms, 37 residues, 20 bonds > show sel atoms > select add #1 2831 atoms, 2890 bonds, 2 pseudobonds, 363 residues, 2 models selected > select subtract #1 Nothing selected > save /Users/h.b/Desktop/gfpnBclosemore res.png width 3000 height 2000 > transparentBackground true supersample 3 '/Users/h.b/Desktop/gfpnBclosemore' has only compression suffix; cannot determine format from suffix > save /Users/h.b/Desktop/gfpnBclosemoreres.png width 3000 height 2000 > transparentBackground true supersample 3 > hide atoms > save /Users/h.b/Desktop/Ginny.cxs ===== Log before crash end ===== Log: Startup Errors --- error | Bundle 'ChimeraX-Clipper' custom initialization failed warning | Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 501, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 ""/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/clipper/__init__.py"", line 32, in __version__ = _version() ^^^^^^^^^^ File ""/Users/h.b/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/clipper/__init__.py"", line 30, in _version return pkg_resources.require('ChimeraX-Clipper')[0].version ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/pkg_resources/__init__.py"", line 937, in require needed = self.resolve(parse_requirements(requirements)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/pkg_resources/__init__.py"", line 798, in resolve dist = self._resolve_dist( ^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/pkg_resources/__init__.py"", line 844, in _resolve_dist raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.8rc202405282004 (/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 375, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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-Core 1.8rc202405282004 (/Applications/ChimeraX-1.8-rc2024.05.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages), Requirement.parse('ChimeraX-Core~=1.8.0'), {'ChimeraX-Clipper'}) UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: MNEH3LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 183 days, 13 hours, 54 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 0.23.1 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: 1.8rc202405282004 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: 1.2.4 ChimeraX-DiffPlot: 1.0 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 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: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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: 3.0.13 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: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.2 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.52.4 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.45 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 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: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.12.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Core duplicate all ChimeraX