id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2539 Clipper prevents session saving satyshur@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.1.2.el7.x86_64-x86_64-with-redhat-7.7-Maipo ChimeraX Version: 0.91 (2019-09-30) Description Trying to change contor levels. Log: UCSF ChimeraX version: 0.91 (2019-09-30) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6d52 format mmCIF fromDatabase pdb structureFactors true Summary of feedback from opening 6d52 fetched from pdb --- warnings | Atom H1 is not in the residue template for GLU #1 in chain B Atom H1 is not in the residue template for GLU #1 in chain D Atom H1 is not in the residue template for GLU #1 in chain C Atom H1 is not in the residue template for GLU #1 in chain A notes | Resolution: 1.4280533552397077 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... 6d52 title: Superoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6 Angstrom resolution [more info...] Chain information for 6d52 --- Chain | Description 1.3/A 1.3/B 1.3/C 1.3/D | Superoxide dismutase [Cu-Zn] 1 Non-standard residues in 6d52 #1.3 --- CU — copper (II) ion ZN — zinc ion 6d52 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > help help:user > camera stereo > camera mono > camera stereo > hide #!1.2 models > show #!1.2 models > hide #!1.3 models > save session /instructor/satyshur/chimera-demo/SodCI/PDB-downloads- peter/start-6d52.cxs Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 794, in save session.save(output, version=version, include_maps=include_maps) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 288, in process return copy_state(data, convert=convert) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 208, in copy_state return _copy(data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 206, in _copy return convert(data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 287, in convert return add_obj(obj, parents) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX- Clipper bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX- Clipper bundle because the class name is not listed in the name to class table for session restore File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 882, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 612, in file_save_cb self.save_dialog.display(self, session) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 139, in display fmt.save(session, filename) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 1089, in save run(session, cmd) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 981, in save_session save(session, filename, **kw) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 220, in export result = self.export_func(session, path, **kw) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 794, in save session.save(output, version=version, include_maps=include_maps) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 288, in process return copy_state(data, convert=convert) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 208, in copy_state return _copy(data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 206, in _copy return convert(data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 287, in convert return add_obj(obj, parents) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX- Clipper bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX- Clipper bundle because the class name is not listed in the name to class table for session restore File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. > ui mousemode rightMode select > ui mousemode rightMode clip > show #!1.3 models > ui mousemode rightMode ""contour level"" Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 458, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 387, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/mouselevel.py"", line 23, in mouse_down self._maps = self._picked_maps(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/mouselevel.py"", line 29, in _picked_maps return self._picked_maps_on_segment(xyz1, xyz2) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/mouselevel.py"", line 37, in _picked_maps_on_segment mxyz1, mxyz2 = ppos * xyz1, ppos * xyz2 File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) TypeError: Cannot multiply Place times ""None"" TypeError: Cannot multiply Place times ""None"" File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.50 OpenGL renderer: Quadro P5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data fixed Tom Goddard all ChimeraX