id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1889 Incorrect ChimeraX version for ISOLDE fabrizio.martino@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.7 (2018-08-07) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.7 (2018-08-07) OpenGL version: 4.1 ATI-1.68.20 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl Downloading bundle ChimeraX_ISOLDE-0.9.24-cp36-cp36m-macosx_10_9_x86_64.whl Traceback (most recent call last):   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/widgets/htmlview.py"", line 366, in download_finished     session=self.session)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 548, in install_bundle     results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 841, in _pip_install     results = self._run_pip(command)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 868, in _run_pip     raise RuntimeError(s) RuntimeError: Processing /Users/martinf/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl Requirement not upgraded as not directly required: ChimeraX-Atomic>=0.7 in /Applications/ChimeraX.app/Contents/lib/python3.6/site-packages (from ChimeraX-ISOLDE==1.0b2) Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2)   Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-macosx_10_9_x86_64.whl (36.1MB) Collecting ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2)   Cache entry deserialization failed, entry ignored   Could not find a version that satisfies the requirement ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) (from versions: ) No matching distribution found for ChimeraX-Core==0.8 (from ChimeraX- ISOLDE==1.0b2) You are using pip version 9.0.3, however version 19.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. RuntimeError: Processing /Users/martinf/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-macosx_10_9_x86_64.whl Requirement not upgraded as not directly required: ChimeraX-Atomic>=0.7 in /Applications/ChimeraX.app/Contents/lib/python3.6/site-packages (from ChimeraX-ISOLDE==1.0b2) Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2) Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3/ChimeraX_Clipper-0.3-cp36-cp36m-macosx_10_9_x86_64.whl (36.1MB) Collecting ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) Cache entry deserialization failed, entry ignored Could not find a version that satisfies the requirement ChimeraX-Core==0.8 (from ChimeraX-ISOLDE==1.0b2) (from versions: ) No matching distribution found for ChimeraX-Core==0.8 (from ChimeraX- ISOLDE==1.0b2) You are using pip version 9.0.3, however version 19.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 868, in _run_pip raise RuntimeError(s) See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. Successfully installed ChimeraX-Clipper-0.3 ChimeraX-ISOLDE-0.9.24 Installed ChimeraX-ISOLDE (0.9.24) toolshed show ISOLDE Traceback (most recent call last):   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 527, in start_tool     ti = api._api_caller.start_tool(api, session, self, tool_info)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 1183, in start_tool     return cls._get_func(api, ""start_tool"")(session, ti.name)   File ""/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/__init__.py"", line 29, in start_tool     return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/tools.py"", line 214, in get_singleton     tinst = tool_class(session, tool_name, **kw)   File ""/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/tool.py"", line 166, in __init__     self.isolde = isolde.Isolde(self)   File ""/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/isolde.py"", line 310, in __init__     self.omega_validator = validation.OmegaValidator(self._annotations)   File ""/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/validation.py"", line 687, in __init__     self._initialize_drawings()   File ""/Users/martinf/Library/Application Support/ChimeraX/0.7/site- packages/chimerax/isolde/validation.py"", line 708, in _initialize_drawings     d.vertices = numpy.zeros([0,3],numpy.float32)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 220, in __setattr__     super(Drawing, self).__setattr__(key, value) AttributeError: can't set attribute During handling of the above exception, another exception occurred: Traceback (most recent call last):   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 846, in     run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name)))   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run     results = command.run(text, log=log)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2561, in run     result = ci.function(session, **kw_args)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show     bi.start_tool(session, tool_name)   File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 533, in start_tool     ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: can't set attribute chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: can't set attribute File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 533, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. OpenGL version: 4.1 ATI-1.68.20 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Third Party can't reproduce Eric Pettersen Conrad Huang all ChimeraX