id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1842 Session save: Unable to restore objects of ImageDrawing class in ChimeraX-Map bundle Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-04-10) Description tried to save solid-rendered volume session I don't think the data matters, but it was emdb 1024 Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > open presets.cxc > alias cardef car style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; car style ~(nucleic|strand) x round; car style (nucleic|strand) x rect > alias nospheres style (protein|nucleic|solvent) & @@draw_mode=0 stick > alias nucrib cardef; car style nucleic x round width 1.6 thick 1.6 > alias cylinders cardef; car style protein modeh tube rad 2 sides 24 thick 0.6 > alias licorice cardef; car style protein modeh default arrows f x round width 1 thick 1 > alias cartoon1 surf hide; nospheres; cartoon; cardef; nuc tube/slab shape box > alias cartoon2 surf hide; nospheres; cartoon; cylinders; car style nucleic x round width 1.6 thick 1.6; nuc stubs > alias cartoon3 surf hide; nospheres; cartoon; licorice; car style nucleic x round width 1.6 thick 1.6; nuc tube/slab shape ellipsoid > alias surfw nospheres; surface; color white targ s trans 80 > alias surfat nospheres; surface; color fromatoms targ s trans 70 > alias surfc nospheres; surface; color bychain targ s trans 0 > alias surfm nospheres; surface; color bymodel targ s trans 0 > alias pub set bgcolor white silhouettes t > alias unpub ~set bgcolor; set silhouettes f executed presets.cxc executed startup.cxc UCSF ChimeraX version: 0.9 (2019-04-10) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Toolbar Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 625, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1476, in start_tool return cls._get_func(api, ""start_tool"")(session, bi, ti) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/__init__.py"", line 17, in start_tool return tool.ToolbarTool(session, ti.name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 49, in __init__ run(session, ""toolshed hide 'Molecule Display Toolbar'"", log=False) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2628, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 357, in toolshed_hide toolshed_show(session, tool_name, _show=False) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 344, in toolshed_show raise UserError('No running tool named ""%s""' % tool_name) chimerax.core.errors.UserError: No running tool named ""Molecule Display Toolbar"" During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 1003, in run(ses, ""toolshed show %s"" % (quote_if_necessary(fave)))) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2628, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/toolshed.py"", line 337, in toolshed_show bi.start_tool(session, tool_name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 631, 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 Toolbar in bundle ChimeraX-Toolbar: No running tool named ""Molecule Display Toolbar"" chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Toolbar in bundle ChimeraX-Toolbar: No running tool named ""Molecule Display Toolbar"" File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 631, 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. > open 2gbp format mmCIF fromDatabase pdb 2gbp title: Sugar and signal-transducer binding sites of the escherichia coli galactose chemoreceptor protein [more info...] Chain information for 2gbp #1 --- Chain | Description A | D-galactose/D-glucose binding protein Non-standard residues in 2gbp #1 --- BGC — β-D-glucose CA — calcium ion > molmap protein 8 > volume selMaps appearance initial > close > open mapicon.cxs opened ChimeraX session > set bgColor black > volume all colormapOnGpu true Expected an objects specifier or a view name or a keyword > view name v1 > volume all dimTransparency false > volume all dimTransparentVoxels false > volume all dimTransparentVoxels true > save blobicon.cxs Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 253, in execute cmd.run(cmd_text) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2628, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 265, in process return copy_state(data, convert=self._add_obj) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 174, in copy_state return _copy(data) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 161, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 161, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/state.py"", line 172, in _copy return convert(data) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 240, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 ImageDrawing class in ChimeraX-Map bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of ImageDrawing class in ChimeraX-Map bundle because the class name is not listed in the name to class table for session restore File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Sessions fixed Greg Couch all ChimeraX