id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2588 Wrong version of Clipper (duplicate of #2214) JMHolton@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.4.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.9 (2019-06-06) Description Launching ISOLDE Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/validation/validation.py"", line 165, in generate_interpolator_data infile = open(os.path.join(cache_dir, file_prefix+'.pickle'), 'r+b') FileNotFoundError: [Errno 2] No such file or directory: '/home/jamesh/.local/share/ChimeraX/0.9/isolde_data/rota8000-val.pickle' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 627, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1435, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/__init__.py"", line 31, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/tools.py"", line 214, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/isolde/tool.py"", line 168, in __init__ self.isolde = isolde.Isolde(self) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 320, in __init__ self._start_gui(gui) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 457, in _start_gui self._populate_menus_and_update_params() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 556, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 1011, in _update_model_list self._change_selected_model(model=current_model) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2412, in _change_selected_model self._update_iffy_rota_list() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/isolde.py"", line 2330, in _update_iffy_rota_list rota_m = get_rotamer_mgr(self.session) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/session_extensions.py"", line 63, in get_rotamer_mgr return Rota_Mgr(session) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 1151, in __init__ self._prepare_all_validators() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 1338, in _prepare_all_validators idata = validation.generate_interpolator_data(data_dir, cache_dir, fname, True) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/validation/validation.py"", line 175, in generate_interpolator_data infile = open(full_path, 'r+t') PermissionError: [Errno 13] Permission denied: '/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/validation/molprobity_data/rota8000-val.data' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1137, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2632, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, 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: [Errno 13] Permission denied: '/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/validation/molprobity_data/rota8000-val.data' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: [Errno 13] Permission denied: '/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/isolde/validation/molprobity_data/rota8000-val.data' File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 633, 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. OpenGL version: 3.3.0 NVIDIA 418.87.01 OpenGL renderer: GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Tool Shed duplicate all ChimeraX