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Opened 6 years ago
Closed 6 years ago
#2999 closed defect (fixed)
Session support missing for Map Eraser
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-5.3.0-42-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.92 (2020-03-08) Description Sometimes when saving session files the error message in the log appears. This is resolved by closing the map eraser sphere object, as well as the map eraser dialogue itself. I have not been able to reproduce this effect is in a simple setup yet. Log: UCSF ChimeraX version: 0.92 (2020-03-08) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200329_cl1-MB-overview.cxs Summary of feedback from opening /home/caillan/Dropbox/rqcH- project/figures/chimerax-sessions/200329_cl1-MB-overview.cxs --- warnings | registering illegal selector name "#1/0" registering illegal selector name "#1/1" registering illegal selector name "1/1" opened ChimeraX session > hide #!1 models Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #4 0 > lighting soft > show #!1 models > hide #!1 models > toolshed show "Map Eraser" Unknown command: ac es > volume erase #4 center 236.83,155.78,170.48 radius 15.436 > hide #5 models > show #5 models > hide #!3 models > show #!1 models > volume erase #6 center 234.11,164.87,193.1 radius 15.326 Unknown command: ac es > volume erase #6 center 239.36,149.86,183.13 radius 15.326 > volume erase #6 center 245.17,192.36,186.5 radius 7.2324 > volume erase #6 center 249.13,191.39,179.88 radius 7.2324 Unknown command: ac es > volume erase #6 center 250.26,195.32,174.01 radius 7.2324 > volume erase #6 center 238.32,235.61,184.28 radius 7.2324 > volume erase #6 center 219.6,268.61,165.71 radius 7.2324 > volume erase #6 center 221.99,266.86,166.57 radius 7.2324 > volume erase #6 center 249.89,231.75,214.36 radius 7.2324 > volume erase #6 center 220.38,235.22,160.58 radius 4.1328 > style stick Changed 8151 atom styles > show atoms > hide atoms > show atoms > show atoms > hide atoms > close #5 > hide #!6 models > show #!6 models > volume #6 level 0.01224 > volume erase #6 center 258.52,236.94,182.27 radius 4.133 > show atoms > close #5 > save /home/caillan/Dropbox/rqcH-project/maps/isolated- > densities/PP_cl1-MB_RqcH-only_job098_manually-cleaned.mrc models #6 > close #5 > close #5 > close #5 > hide atoms > view list Named views: CC-view > view CC-view > surface dust #6 > show #!4 models > hide #!4 models > close #4 > volume #6 level 0.01468 > hide #!1 models > lighting full > lighting soft > volume #6 level 0.0145 > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_CC-view-density.png width 1500 height 1300 > transparentBackground true > show #!1 models > hide #!6 models > lighting flat > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_CC-view-cartoon.png width 1500 height 1300 > transparentBackground true > show #!6 models > lighting full > lighting soft Unknown command: tranparency #6 0.5 > transparency #6 0.5 > lighting simple > transparency #6 0.5 > hide #!6 models > show #!6 models > transparency #6 0.2 > transparency #6 0.5 > lighting soft > lighting simple > show #!3 models > hide #!3 models > hide #!6 models > show #!3 models > show #!3.1 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > hide #!3 models > hide #!3.1 models > show #!2 models > hide #!2 models > close #2 > show #!6 models > transparency #6 0.5 > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_CC-view-transparent-model.png width 1500 height 1300 > transparentBackground true > lighting soft > lighting flat > lighting full > lighting simple > lighting soft > lighting full > lighting flat > lighting full > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > hide #!6 models > show #!6 models > graphics silhouettes true > lighting flat > hide #!6 models > show #!6 models > hide #!6 models > view name glob-view > view list Named views: CC-view, glob-view > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_glob-view-cartoon.png width 1500 height 1300 > transparentBackground true > show #!6 models > hide #!1 models > lighting soft > toolshed show "Side View" > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_glob-view-density.png width 1500 height 1300 > transparentBackground true > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs > show #!1 models > hide #!6 models > show #!6 models > color zone #4 near NFACT-N > color zone #6 near NFACT-N > color zone #6 near NFACT-N distance 3 > color zone #6 near HhH distance 3 > color zone #6 near NFACT-N distance 3 > volume splitbyzone #6 > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2.2 models > show #!2.2 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > select up Nothing selected > color zone #6 near HhH distance 3 > show #!6 models > hide #!2 models > select up Nothing selected > volume splitbyzone #6 > hide #!4 models > show #!4 models > close #4 > show #!6 models > color zone #6 near HhH distance 4 > volume splitbyzone #6 > hide #!4 models > show #!6 models > color zone #6 near CC-M distance 4 > volume splitbyzone #6 > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > color zone #6 near NFACT-R distance 4 > volume splitbyzone #6 > hide #!7.1 models > hide #!7 models > show #!6 models > hide #!6.1 models > show #!6.1 models > hide #!6.1 models > show #!6.1 models > hide #!6 models > show #!5 models > hide #!5.1 models > show #!7 models > hide #!7 models > show #!7 models > show #!4 models > hide #!4.1 models > show #!3.1 models > hide #!3.1 models > show #!2 models > show #!2.1 models > hide #!2.1 models > surface dust #2 > surface dust #4 > surface dust #5 > surface dust #7 > hide #!1 models > view CC-view > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_CC-view-coloured-density.png width 1500 height 1300 > transparentBackground true > close #2.1 > close #4.1 > close #5.1 > close #7.1 > view glob-view > volume #4.2 level 0.01491 > volume #4.2 level 0.0145 > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!7 models > hide #!5 models > show #!5 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!5 models > show #!5 models > show #!6 models > hide #!6 models > hide #!7 models > show #!7 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!2 models > view glob-view > hide #!1 models > show #!2 models > select up Nothing selected > select down Nothing selected > select up Nothing selected > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_glob-view-coloured-density.png width 1500 height 1300 > transparentBackground true > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!7 models > show #!6 models > show #!1 models > hide #!1 models > show #!3 models > hide #!6 models > show #!3.1 models > show #!3.2 models > hide #!3.2 models > hide #!3.1 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > show #!3.1 models > show #!3.2 models > close #3 > open /home/caillan/Dropbox/rqcH-project/maps/multibody- > maps/postprocessed_EPA-cl1-w-stalk/EPA-cl1_RqcH-w-stalk_MB_job098/EPA- > cl1_RqcH-w-stalk_MB_job098_postprocess_masked.mrc Opened EPA-cl1_RqcH-w-stalk_MB_job098_postprocess_masked.mrc, grid size 420,420,420, pixel 0.82, shown at level 3.69e-06, step 2, values float32 > volume #3 level 0.01935 > volume #3 step 1 > volume #3 level 0.0145 > volume #3 color #babdb6 > transparency #3 0.5 > lighting soft > show #!1 models > transparency #3 0.5 > transparency #3.1 0.5 > lighting soft > close #8 > lighting soft > lighting full > hide #3.1 models > show #3.1 models > surface dust #3 > show cartoons > hide #!3 models > select /0:377 11 atoms, 11 bonds, 1 model selected > show sel atoms > select /A:1113 22 atoms, 24 bonds, 1 model selected > show sel atoms > select clear > show #1.1 models > hide #1.1 models > show #!3 models > volume #3 level 0.01732 > lighting shadows false > select /A:1113 22 atoms, 24 bonds, 1 model selected > select up 1801 atoms, 2011 bonds, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 1801 atom styles > show sel atoms > select clear > lighting soft > lighting full > lighting flat > lighting full > lighting shadows false > select /A:1113 22 atoms, 24 bonds, 1 model selected > select up 1801 atoms, 2011 bonds, 1 model selected > hide sel atoms > select clear > select /A:1113 22 atoms, 24 bonds, 1 model selected > show sel atoms > select clear > select /A:1113@C2 1 atom, 1 model selected > color sel byhetero > style sel stick Changed 1 atom style > nucleotides sel fill > style nucleic & sel stick Changed 1 atom style > nucleotides sel atoms > style nucleic & sel stick Changed 1 atom style > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > color sel byhetero > color sel byelement > select clear > hide #!3 models > select /A:1113@N3 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > color sel byelement > select clear > show #!3 models > select /0:382 9 atoms, 8 bonds, 1 model selected > select up 349 atoms, 354 bonds, 1 model selected > show sel cartoons > show sel atoms > hide sel atoms > select clear > select /0:377 11 atoms, 11 bonds, 1 model selected > show sel atoms > select clear > toolshed show "Map Eraser" > volume erase #3 center 233.04,249.92,173.09 radius 22.332 outside true > toolshed show "Volume Viewer" > toolshed show "Map Eraser" > volume erase #9 center 228.77,275.88,166.79 radius 18.596 > close #8 > select /A:2502 20 atoms, 21 bonds, 1 model selected > select /A:2501 23 atoms, 25 bonds, 1 model selected > hide sel cartoons > hide sel cartoons > toolshed show "Map Eraser" > volume erase #9 center 237.11,259.26,160.98 radius 10.042 > volume erase #9 center 208.93,258.93,170.22 radius 10.042 > surface dust #9 > hide #8 models > select /A:1114 23 atoms, 25 bonds, 1 model selected > show sel atoms > select up 1801 atoms, 2011 bonds, 1 model selected > select down 23 atoms, 25 bonds, 1 model selected > color sel byelement > select clear > select /K:33 7 atoms, 6 bonds, 1 model selected > select up 41 atoms, 40 bonds, 1 model selected > select up 975 atoms, 989 bonds, 1 model selected Expected ',' or a keyword > hide sel cartoons > select clear > hide sel cartoons > select clear > select /A:1112 20 atoms, 21 bonds, 1 model selected > show sel atoms > hide #!9 models > show sel atoms > select clear > select clear > color sel byelement > select clear > show #!9 models > hide sel cartoons > select clear > show sel cartoons > show sel atoms > color sel byelement > select clear > volume #9 level 0.01474 > hide sel cartoons > select clear > volume #9 level 0.01787 > hide sel atoms > hide #!1 models > show #!1 models > hide #!9 models > hide sel atoms > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!9 models > select clear > select /1:36 9 atoms, 8 bonds, 1 model selected > select up 140 atoms, 140 bonds, 1 model selected > hide sel cartoons > select clear > select up 1801 atoms, 2011 bonds, 1 model selected > select down 20 atoms, 1 model selected > select clear > hide sel cartoons > show #!3 models > hide #!1 models > show #!1 models > show #1.1 models > hide #1.1 models > hide #!1 models > show #!1 models > hide #!3 models > view name phe377 > view name phe377-close > lighting flat > lighting full > lighting soft > lighting simple > graphics silhouettes false > graphics silhouettes true > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_phe377-close.png width 1500 height 1300 > transparentBackground true > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_phe377-close.png width 1500 height 1300 > transparentBackground true > view name phe377-close > show #!5 models > hide #!5 models > hide #!9 models > show #!9 models > hide #!9 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!9 models > hide #!9 models > hide #!1 models > show #!1 models > show #1 cartoons > view phe377 > view phe377-close > select /K:47 5 atoms, 4 bonds, 1 model selected > select up 46 atoms, 45 bonds, 1 model selected > select up 975 atoms, 989 bonds, 1 model selected Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel darkgrey > select clear > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 935, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 651, in file_save_cb self.save_dialog.display(self, session) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 1100, in save run(session, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2845, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 992, in save_session save(session, filename, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 229, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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. > hide #!1 models > show #1.1 models > hide #1.1 models > show #!2 models > hide #!1 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > save /home/caillan/Dropbox/rqcH-project/maps/isolated- > densities/PP_cl1-MB_NFACT-N-rough_job098.mrc models #2.2 > hide #!2 models > show #!2 models > hide #!2.2 models > show #!2.2 models > hide #!6 models > hide #!2 models > hide #!3 models > show #!3 models > show #!4 models > save /home/caillan/Dropbox/rqcH-project/maps/isolated- > densities/PP_cl1-MB_HhH-rough_job098.mrc models #4.2 > hide #!3 models > show #!5 models > hide #!4 models > show #!3 models > save /home/caillan/Dropbox/rqcH-project/maps/isolated- > densities/PP_cl1-MB_CC-M-rough_job098.mrc models #5.2 > show #!6 models > hide #!6 models > show #!7 models > save /home/caillan/Dropbox/rqcH-project/maps/isolated- > densities/PP_cl1-MB_NFACT-R_job098.mrc models #7.2 > hide #!5 models > hide #!7 models > show #!1 models > color NFACT-N tan > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > select /2:42 23 atoms, 25 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > color sel skyblue > select clear > select clear > nucleotides sel atoms > style nucleic & sel stick Changed 316 atom styles > show sel atoms > select clear > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #!3 models > hide #!3 models > show #!3 models > select clear > view CC-view > select clear > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > hide #!1 models > show #1.1 models > hide cartoons > hide atoms Expected ',' or a keyword Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #1/0 cartoons > select clear > lighting flat > view CC-view > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_CC-view-cartoon.png width 1500 height 1300 > transparentBackground true > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > hide #!6 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #8 models > show #!9 models > hide #!9 models > hide #8 models > show #!6 models > hide #!6 models > show #!1 models > hide #!1 models > show #!2 models > hide #!4 models > show #!4 models > hide #!2 models > show #!2 models > color #2.1 tan > color #2 tan > volume #5.2 level 0.01557 > volume #4.2 level 0.01471 > volume #4.2 level 0.0145 > volume #5.2 level 0.015 > lighting soft > lighting full > lighting simple > lighting soft > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_CC-view-density.png width 1500 height 1300 > transparentBackground true > view glob-view > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_glob-view-density.png width 1500 height 1300 > transparentBackground true > hide #!2 models > hide #!4 models > hide #!5 models > hide #!7 models > show #!1 models > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_glob-view-cartoon.png width 1500 height 1300 > transparentBackground true > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 935, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 651, in file_save_cb self.save_dialog.display(self, session) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 1100, in save run(session, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2845, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 992, in save_session save(session, filename, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 229, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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. > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 935, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 651, in file_save_cb self.save_dialog.display(self, session) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 1100, in save run(session, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2845, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 992, in save_session save(session, filename, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 229, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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. > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs > close session > open /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_cl1-MB-overview.cxs Summary of feedback from opening /home/caillan/Dropbox/rqcH- project/figures/chimerax-sessions/200330_cl1-MB-overview.cxs --- warnings | registering illegal selector name "#1/0" registering illegal selector name "#1/1" registering illegal selector name "1/1" opened ChimeraX session > toolshed show "Map Eraser" > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_test.cxs > close #8 > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_test.cxs > view phe377-close > hide #!1 models > show #!1 models > show #1/A cartoons > close #8 > hide #1.1 models > sequence chain #1/A Alignment identifier is 1.A > select clear > select /A:1113 22 atoms, 24 bonds, 1 model selected > select clear > select clear > show sel atoms > hide sel atoms > show sel cartoons > name sel foo "sel" is reserved and cannot be redefined > name foo sel > select clear > color foo blue > select foo Nothing selected > show cartoons > hide sel cartoons > select /0:377 11 atoms, 11 bonds, 1 model selected > show sel atoms > select /A:1113 22 atoms, 24 bonds, 1 model selected > show sel atoms > select clear > select clear > select /0:527 5 atoms, 4 bonds, 1 model selected > select up 35 atoms, 34 bonds, 1 model selected > select up 3986 atoms, 4051 bonds, 1 model selected > select down 35 atoms, 34 bonds, 1 model selected > select down 5 atoms, 4 bonds, 1 model selected > select clear > hide NFACT-R cartoons > select clear > select /K:36 8 atoms, 7 bonds, 1 model selected > select clear > select /A:1140 20 atoms, 21 bonds, 1 model selected > select up 1801 atoms, 2011 bonds, 1 model selected > color sel lightgrey > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > color sel byelement > select clear > select /K:23 7 atoms, 7 bonds, 1 model selected > show sel atoms > select clear > select /K:22 7 atoms, 7 bonds, 1 model selected > show sel atoms > select clear > select /K:27 5 atoms, 4 bonds, 1 model selected > select clear > select /K:27 5 atoms, 4 bonds, 1 model selected > select up 28 atoms, 28 bonds, 1 model selected > select up 975 atoms, 989 bonds, 1 model selected > select down 28 atoms, 28 bonds, 1 model selected > select down 5 atoms, 4 bonds, 1 model selected > select down 5 atoms, 4 bonds, 1 model selected > select clear > select /A:1114 23 atoms, 25 bonds, 1 model selected > show sel atoms > select /A:1115 22 atoms, 24 bonds, 1 model selected > show sel atoms > hide sel atoms > select clear > show #1.1 models > hide #1.1 models > show #!9 models > hide #!9 models > show #1.1 models > hide #1.1 models > show #!3 models > hide #!3 models > show #!3 models > lighting simple > toolshed show "Map Eraser" > volume erase #3 center 248.24,230.97,215.19 radius 24.891 > volume erase #10 center 260.5,236.87,203.84 radius 24.797 > volume erase #10 center 275.66,233.59,186.84 radius 24.797 > volume erase #10 center 250.67,233.68,209.51 radius 24.797 > volume erase #10 center 238.62,233.54,185.73 radius 7.2324 > hide #8 models > surface dust #10 > toolshed show "Side View" > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_Phe377.cxs > show #1 cartoons > undo > volume erase #10 center 191.22,246.62,180.5 radius 7.2324 > volume erase #10 center 190.02,247.33,166.42 radius 11.021 > volume erase #10 center 202.13,235.48,176.79 radius 11.021 > volume erase #10 center 202.94,237.15,172.89 radius 11.021 > volume erase #10 center 193.36,245.65,157.04 radius 11.021 > volume erase #10 center 198.69,249.2,144.84 radius 11.021 > volume erase #10 center 200.77,242.65,141.16 radius 11.021 > view list Named views: CC-view, glob-view, phe377, phe377-close > view phe377 > view phe377-close > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > view phe377-close > view phe377-close > close #8 > select /2:36 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > show sel atoms > select clear > select up 2 atoms, 1 bond, 1 model selected > select clear > close #8 > undo > undo > close #8 > select /0:125 11 atoms, 10 bonds, 1 model selected > select clear > select /2:36@C1' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > color sel byelement > select clear > select /2:34 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > color sel skyblue > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > transparency sel 0.5 > hide #!10 models > select clear > select /0:125 11 atoms, 10 bonds, 1 model selected > show sel atoms > color sel byhetero > select clear > nucleotides fill > style nucleic stick Changed 2531 atom styles > nucleotides fill > style nucleic stick Changed 2531 atom styles > nucleotides fill > style nucleic stick Changed 2531 atom styles > nucleotides tube/slab shape box > nucleotides atoms > style nucleic stick Changed 2531 atom styles > select /2:36@C2' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > select down 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > name sel tRNA "sel" is reserved and cannot be redefined > name tRNA sel > color tRNA blue > color tRNA skyblue > color tRNA byhetero > select clear > select /2:36@N1 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > select down 20 atoms, 21 bonds, 1 model selected > name sel C36 "sel" is reserved and cannot be redefined > name C36 sel > select clear Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color C36 green > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 1 atoms > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > transparency 0.5 atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 0.5 bonds Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword Expected ',' or a keyword Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' > transparency tRNA 1 atoms > transparency tRNA 1 bonds > transparency tRNA 1 cartoons > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select clear > select /0:277 11 atoms, 11 bonds, 1 model selected > transparency sel 1 cartoons > select clear > select clear > select /A:1950 23 atoms, 25 bonds, 1 model selected > select clear > show #1.1 models > hide #1.1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > save /home/caillan/Desktop/text-trans.png > transparency sel 0 cartoons > transparency tRNA 0 cartoons > show #!3 models > hide #!3 models Drag select of 585 atoms, 735 residues, 641 bonds > transparency sel 0 > transparency sel 0 cartoons > transparency sel 0 bonds > transparency sel 0 atoms > select clear > graphics silhouettes false > graphics silhouettes true > hide sel cartoons > show sel cartoons Missing or invalid "percent" argument: Expected a number > transparency 0 All Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #10 0.5 > volume #10 color #c9c9c946 > select /2:36@N1 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select up 730 atoms, 815 bonds, 1 model selected > select down 20 atoms, 21 bonds, 1 model selected Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel cartoons > show sel cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel bonds > show sel bonds > select clear > close #9 > volume #10 level 0.02079 > transparency tRNA 0.5 bonds > listinfo names Expected a models specifier or a keyword Unknown command: names list Unknown command: names > name list C36 sel CC-M #1/0:282-434 HhH #1/0:179-281 NFACT-N #1/0:3-173 NFACT-R #1/0:446-565 foo sel tRNA sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color C36 grey bonds > lighting soft > volume #10 level 0.01914 > select /A:1949 20 atoms, 21 bonds, 1 model selected > select up 1801 atoms, 2011 bonds, 1 model selected > hide sel cartoons > select clear > select up Nothing selected > select down Nothing selected > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_R125-view.png width 1500 height 1300 transparentBackground > true > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_R125-view.png width 1500 height 1300 transparentBackground > true > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_R125-view.png width 1500 height 1300 transparentBackground > true > select /2:36@N1 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > hide sel atoms > select clear > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_R125-view-no-C36.png width 1500 height 1300 > transparentBackground true > show sel atoms > show sel bonds > undo > undo > undo > undo > color sel grey > color sel lightgrey > select clear > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_R125-view-grey-C36.png width 1500 height 1300 > transparentBackground true > select /2:36@N1 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > color sel lightgrey cartoons > color sel skyblue cartoons > select clear > select up Nothing selected > select down Nothing selected > save /home/caillan/Dropbox/rqcH-project/figures/MB-RqcH-domains- > overview/200329_R125-view-grey-C36.png width 1500 height 1300 > transparentBackground true > view name R125-view > save session /home/caillan/Dropbox/rqcH-project/figures/chimerax- > sessions/200330_Arg125.cxs Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 935, in <lambda> save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py", line 651, in file_save_cb self.save_dialog.display(self, session) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 139, in display fmt.save(session, filename) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 1100, in save run(session, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2845, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 992, in save_session save(session, filename, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/core/io.py", line 229, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 796, in save session.save(output, version=version, include_maps=include_maps) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 556, in save mgr.discovery(self._state_containers) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 255, in discovery self.processed[key] = self.process(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 288, in process return copy_state(data, convert=convert) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 210, in copy_state return _copy(data) File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 195, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/state.py", line 208, in _copy return convert(data) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 287, in convert return add_obj(obj, parents) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/session.py", line 261, in _add_obj uid = _UniqueName.from_obj(self.session, obj) File "/usr/lib/ucsf-chimerax/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 SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore RuntimeError: Unable to restore objects of SphereModel class in ChimeraX- MapEraser bundle because the class name is not listed in the name to class table for session restore File "/usr/lib/ucsf-chimerax/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: 4.5 (Core Profile) Mesa 19.2.8 OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) OpenGL vendor: Intel Open Source Technology Center
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session support missing for Map Eraser |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
The error saving a session with the map eraser sphere showing only happened if a named view was made that included the map eraser sphere. I made session save of views not save models that are not saved in sessions such as the map eraser sphere.
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Reported by Cailan Crowe-McAuliffe