id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1846 Either: Tempy broken, or Registration internal error -- dealer's choice chimerax-bug-report@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-46-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.8 (2018-11-28) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 338, in __init__ self.init_available_from_cache(logger) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 445, in init_available_from_cache abc.load_from_cache() File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 61, in load_from_cache b = _build_bundle(d) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/available.py"", line 242, in _build_bundle keywords = _extract_extra_keywords(keywords) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/installed.py"", line 270, in _extract_extra_keywords all_kwds = [k.strip() for k in kwds.split(',')] AttributeError: 'list' object has no attribute 'split' UCSF ChimeraX version: 0.8 (2018-11-28) How to cite UCSF ChimeraX > open /home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.yob Unrecognized file suffix '.yob' Unrecognized file suffix '.yob' > open /home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.pdb Summary of feedback from opening /home/ricardo/tilipo33_publicação/dock_files/yasara/tilipo33_model-1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK YASARA ************************************************************* Ignored bad PDB record found on line 2 REMARK YASARA * * Ignored bad PDB record found on line 3 REMARK YASARA * Y A S A R A * Ignored bad PDB record found on line 4 REMARK YASARA * * Ignored bad PDB record found on line 5 REMARK YASARA * Yet Another Scientific Artificial Reality Application * 14 messages similar to the above omitted Chain information for tilipo33_model-1.pdb #1 --- Chain | Description A | biogenic amine-binding protein > ~select #1 Nothing selected > select #1 2617 atoms, 2644 bonds selected > ~select #1 Nothing selected > hide selAtoms ribbons > toolshed show ""Blast Protein"" Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service Opal job id: appBlastProtein2Service15553544029431093310020 Opal status URL: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15553544029431093310020 BlastProtein finished. > hide selAtoms ribbons > show selAtoms > show selAtoms ribbons > hide selAtoms ribbons > show selAtoms ribbons > hide selAtoms > show selAtoms > lighting full > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting simple > hide selAtoms ribbons > ui mousemode rightMode rotate and select > ui mousemode rightMode translate > ui mousemode rightMode select > ui mousemode rightMode clip > ui mousemode rightMode distance > ui mousemode rightMode tug > ui mousemode rightMode minimize > hide selAtoms ribbons > hide selAtoms > show selAtoms ribbons Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl Successfully installed ChimeraX-Clipper-0.3.1 ChimeraX-ISOLDE-1.0b2 Installed ChimeraX-Clipper (0.3.1) Installed ChimeraX-ISOLDE (1.0b2) Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl Successfully installed ChimeraX-Cytoscape-0.1 Installed ChimeraX-Cytoscape (0.1) Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl Successfully installed ChimeraX-Stringdb-0.1 Installed ChimeraX-Stringdb (0.1) Downloading bundle ChimeraX_Stringdb-0.1-py3-none-any.whl unloading module chimerax.stringdb Successfully installed ChimeraX-Stringdb-0.1 Installed ChimeraX-Stringdb (0.1) Downloading bundle ChimeraX_BlastProtein-0.1-py3-none-any.whl unloading module chimerax.blastprotein Successfully installed ChimeraX-BlastProtein-0.1 Installed ChimeraX-BlastProtein (0.1) Downloading bundle ChimeraX_Tempy-0.6.0-py3-none-any.whl unloading module chimerax.tempy Successfully installed ChimeraX-Tempy-0.6.0 Installed ChimeraX-Tempy (0.6.0) > toolshed show ""Blast Protein"" > toolshed show ""Density Map Toolbar"" > close session > open ""/media/ricardo/New Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_299.pdb"" Chain information for AaTI_Structure_refine_299.pdb #1 --- Chain | Description A | No description available B | No description available > open ""/media/ricardo/New Volume/home/ricardo/aati/pedro_aati/AaTI/Refine_299/AaTI_Structure_refine_data.mtz"" Must specify a structure model to associate with crystallographic data Must specify a structure model to associate with crystallographic data > volume selMaps style solid No volumes specified No volumes specified > toolshed show Tempy Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 575, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/__init__.py"", line 1185, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""/home/ricardo/.local/share/ChimeraX/0.8/site- packages/chimerax/tempy/__init__.py"", line 16, in start_tool from .tool import ToolUI File ""/home/ricardo/.local/share/ChimeraX/0.8/site- packages/chimerax/tempy/tool.py"", line 14, in from . import tool_scores File ""/home/ricardo/.local/share/ChimeraX/0.8/site- packages/chimerax/tempy/tool_scores.py"", line 8, in from . import tool_select File ""/home/ricardo/.local/share/ChimeraX/0.8/site- packages/chimerax/tempy/tool_select.py"", line 8, in from chimerax.core.map.volume import Volume ModuleNotFoundError: No module named 'chimerax.core.map' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 922, in run(ses, ""toolshed show %s"" % quote_if_necessary(tool_name))) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2581, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 581, 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 Tempy in bundle ChimeraX-Tempy: No module named 'chimerax.core.map' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Tempy in bundle ChimeraX-Tempy: No module named 'chimerax.core.map' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/core/toolshed/info.py"", line 581, 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. > volume selMaps style mesh No volumes specified No volumes specified > select #1 927 atoms, 844 bonds selected > volume selMaps style solid No volumes specified No volumes specified > ~select #1 Nothing selected > toolshed show Registration Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 529, in customEvent func(*args, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/registration/gui.py"", line 67, in handle_scheme self.session.ui.thread_safe(self._register, url) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 286, in thread_safe func(*args, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/registration/gui.py"", line 121, in _register join_announcements=values[""join_announcements""]) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/registration/cmd.py"", line 76, in register funding, funding_other, comment) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/site- packages/chimerax/registration/cmd.py"", line 120, in _get_registration with urlopen(RegistrationURL, urlencode(params).encode()) as f: File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 223, in urlopen return opener.open(url, data, timeout) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 532, in open response = meth(req, response) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 642, in http_response 'http', request, response, code, msg, hdrs) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 570, in error return self._call_chain(*args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 504, in _call_chain result = func(*args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 650, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 500: Registration internal error urllib.error.HTTPError: HTTP Error 500: Registration internal error File ""/usr/lib/ucsf-chimerax-daily/lib/python3.6/urllib/request.py"", line 650, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Infrastructure wontfix Tom Goddard all ChimeraX