Opened 23 months ago
Closed 23 months ago
#10332 closed defect (duplicate)
Unable to restore objects of NewerVersionQuery class
Reported by: | Owned by: | Zach Pearson | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sessions | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.7.dev202310042257 (2023-10-04 22:57:21 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.7.dev202310042257 (2023-10-04) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3fmg Summary of feedback from opening 3fmg fetched from pdb --- note | Fetching compressed mmCIF 3fmg from http://files.rcsb.org/download/3fmg.cif 3fmg title: Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab [more info...] Chain information for 3fmg #1 --- Chain | Description | UniProt A | Glycoprotein VP7 | VS09_ROTHR 51-326 H | Fab of neutralizing antibody 4F8, heavy chain | L | Fab of neutralizing antibody 4F8, light chain | Non-standard residues in 3fmg #1 --- CA — calcium ion 3fmg mmCIF Assemblies --- 1| author_defined_assembly > open 3fmg fromDatabase pdbe_bio Summary of feedback from opening 3fmg fetched from pdbe_bio --- warning | Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. note | Fetching compressed 3fmg bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/3fmg-assembly-1.cif.gz 3fmg bioassembly 1 title: Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab [more info...] Chain information for 3fmg bioassembly 1 #2 --- Chain | Description A AA AB | Fab of neutralizing antibody 4F8, light chain B BA BB | Fab of neutralizing antibody 4F8, heavy chain C CA CB | Glycoprotein VP7 Non-standard residues in 3fmg bioassembly 1 #2 --- CA — (CA) 3fmg bioassembly 1 mmCIF Assemblies --- 1| author_defined_assembly Opened 1 biological assemblies for 3fmg > hide #!1 models > hide #2 models > show #2 models > close #1 > hide atoms > show cartoons > open > C:/Users/pb099337/Downloads/vp7_clustalo-I20231212-211330-0663-45787566-p1m.aln Summary of feedback from opening C:/Users/pb099337/Downloads/vp7_clustalo-I20231212-211330-0663-45787566-p1m.aln --- notes | Alignment identifier is vp7_clustalo-I20231212-211330-0663-45787566-p1m.aln Associated 3fmg bioassembly 1 chain C to AU1_VP7 with 13 mismatches Associated 3fmg bioassembly 1 chain CA to AU1_VP7 with 13 mismatches Associated 3fmg bioassembly 1 chain CB to AU1_VP7 with 13 mismatches Showing conservation header ("seq_conservation" residue attribute) for alignment vp7_clustalo-I20231212-211330-0663-45787566-p1m.aln Opened 4 sequences from vp7_clustalo-I20231212-211330-0663-45787566-p1m.aln > color byconservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byattribute seq_conservation 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette rainbow 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 Fetching compressed palette white,red,blue from https://www.colourlovers.com/api/palettes?keywords=white%2Cred%2Cblue&format=json&numResults=100 Could not find palette white,red,blue at COLOURlovers.com using keyword search > preset pub Multiple preset names match 'pub': publication 1 (silhouettes); publication 2 (depth-cued) > color byattribute seq_conservation 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > select /CB:126 6 atoms, 5 bonds, 1 residue, 1 model selected > select /CB:157 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /CB:124 8 atoms, 7 bonds, 1 residue, 1 model selected > select /CB:125 5 atoms, 4 bonds, 1 residue, 1 model selected > color byattribute seq_conservation palette gray 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette white:yellow:tomato 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette tomato:yellow:white 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette red:yellow:white 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > select clear > select /C-CB:107 24 atoms, 21 bonds, 3 residues, 1 model selected > select /C-CB:107 24 atoms, 21 bonds, 3 residues, 1 model selected > select /CA:111 14 atoms, 15 bonds, 1 residue, 1 model selected > select /CA:107 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /CA:111 22 atoms, 22 bonds, 2 residues, 1 model selected > color byattribute seq_conservation palette red:orange:yellow:white 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > select /CA:96 8 atoms, 7 bonds, 1 residue, 1 model selected > color byattribute seq_conservation palette magenta:red:orange:yellow:white 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > select clear [Repeated 1 time(s)] > select /C:190 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select /C:190 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:193 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /C:223 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:188 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:190 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select /C:188 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > color byattribute seq_conservation palette magenta:white 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette red:yellow:white 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > select clear > select /C:242 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:190 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:188 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C:186 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:186 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:225 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:186 6 atoms, 5 bonds, 1 residue, 1 model selected > select /C:220 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /C:220 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /C:219 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select /C:220 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /C:221 5 atoms, 4 bonds, 1 residue, 1 model selected > select /C:220 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /C:220 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:219 5 atoms, 4 bonds, 1 residue, 1 model selected > select /C:218 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > lighting soft > graphics silhouettes true > set bgColor white > color byattribute seq_conservation palette red:yellow:dark 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette red:yellow:gray 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > color byattribute seq_conservation palette red:yellow:darkgray 15498 atoms, 2007 residues, atom seq_conservation range -2.75 to 0.67 > open 3fmg fromdatabase:pdbe_bio No such database 'fromdatabase' > open 3fmg fromDatabase pdbe_bio Summary of feedback from opening 3fmg fetched from pdbe_bio --- warning | Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 3fmg bioassembly 1 title: Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab [more info...] Chain information for 3fmg bioassembly 1 #1 --- Chain | Description A AA AB | Fab of neutralizing antibody 4F8, light chain B BA BB | Fab of neutralizing antibody 4F8, heavy chain C CA CB | Glycoprotein VP7 Non-standard residues in 3fmg bioassembly 1 #1 --- CA — (CA) 3fmg bioassembly 1 mmCIF Assemblies --- 1| author_defined_assembly Associated 3fmg bioassembly 1 chain C to AU1_VP7 with 13 mismatches Associated 3fmg bioassembly 1 chain CA to AU1_VP7 with 13 mismatches Associated 3fmg bioassembly 1 chain CB to AU1_VP7 with 13 mismatches Opened 1 biological assemblies for 3fmg > open 3fmg fromDatabase pdbe_bio Summary of feedback from opening 3fmg fetched from pdbe_bio --- warning | Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 3fmg bioassembly 1 title: Structure of rotavirus outer capsid protein VP7 trimer in complex with a neutralizing Fab [more info...] Chain information for 3fmg bioassembly 1 #3 --- Chain | Description A AA AB | Fab of neutralizing antibody 4F8, light chain B BA BB | Fab of neutralizing antibody 4F8, heavy chain C CA CB | Glycoprotein VP7 Non-standard residues in 3fmg bioassembly 1 #3 --- CA — (CA) 3fmg bioassembly 1 mmCIF Assemblies --- 1| author_defined_assembly Associated 3fmg bioassembly 1 chain C to AU1_VP7 with 13 mismatches Associated 3fmg bioassembly 1 chain CA to AU1_VP7 with 13 mismatches Associated 3fmg bioassembly 1 chain CB to AU1_VP7 with 13 mismatches Opened 1 biological assemblies for 3fmg > hide #3 models > hide #2 models > hide #1 models > show #1 models > hide #1 models > show #2 models > show #3 models > hide #3 models > close #3 > hide #2 models > show #1 models Drag select of 225 atoms > lighting simple > select up 376 atoms, 364 bonds, 47 residues, 1 model selected > select up 1003 atoms, 1017 bonds, 126 residues, 1 model selected > select up 3720 atoms, 3798 bonds, 470 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 500 atoms > select up 611 atoms, 612 bonds, 77 residues, 1 model selected > select up 1321 atoms, 1347 bonds, 164 residues, 1 model selected > select up 1860 atoms, 1899 bonds, 235 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > hide #1 atoms > show #1 cartoons > show #2 models > hide #1 models Drag select of 726 residues > select up 6298 atoms, 6435 bonds, 834 residues, 1 model selected > select up 9912 atoms, 10173 bonds, 1296 residues, 1 model selected > delete atoms sel > delete bonds sel > show #1 models > hide #1 models > hide #2 models > show #2 models > style #2 sphere Changed 5586 atom styles > show #2 atoms > show #2 cartoons > hide #2 atoms > select add #2 5586 atoms, 5697 bonds, 711 residues, 1 model selected > surface sel > show #1 models > hide #!2 models > show #!2 models > color #2 byattr seq_conservation palette red:yellow:darkgray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byattribute seq_conservation palette red:yellow:darkgray 15504 atoms, 2013 residues, 3 surfaces, atom seq_conservation range -2.75 to 0.67 > select clear > select add #2 5586 atoms, 5697 bonds, 711 residues, 1 model selected > select add #1 15504 atoms, 15870 bonds, 2013 residues, 5 models selected > select subtract #2 9918 atoms, 10173 bonds, 1302 residues, 4 models selected > select add #2 15504 atoms, 15870 bonds, 2013 residues, 2 models selected > select subtract #2 9918 atoms, 10173 bonds, 1302 residues, 4 models selected > select add #2 15504 atoms, 15870 bonds, 2013 residues, 2 models selected > select subtract #1 5586 atoms, 5697 bonds, 711 residues, 4 models selected > select subtract #2 3 models selected > select add #1 9918 atoms, 10173 bonds, 1302 residues, 1 model selected > select subtract #1 Nothing selected > select add #2 5586 atoms, 5697 bonds, 711 residues, 1 model selected > surface hidePatches (#!2 & sel) > save C:/Users/pb099337/Documents/rotavirus_vp7_strains-conservation.cxs Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 901, in save session.save(output, version=version, include_maps=include_maps) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 625, in save mgr.discovery(self._state_containers) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at 0x0000020EA9223310>: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 51, in display run(session, cmd) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 90, in provider_save saver_info.save(session, path, **provider_kw) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 84, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 901, in save session.save(output, version=version, include_maps=include_maps) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 625, in save mgr.discovery(self._state_containers) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at 0x0000020EA9223310>: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > select clear > save C:/Users/pb099337/Documents/rotavirus_strains_vp7.cxs Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 901, in save session.save(output, version=version, include_maps=include_maps) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 625, in save mgr.discovery(self._state_containers) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at 0x0000020EA9223310>: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 299, in process return copy_state(data, convert=convert) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 219, in copy_state return _copy(data) ^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 204, in <listcomp> items = [(_copy(k), _copy(v)) for k, v in data.items()] ^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\state.py", line 217, in _copy return convert(data) ^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 298, in convert return add_obj(obj, parents) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 270, in _add_obj uid = _UniqueName.from_obj(self.session, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 143, in from_obj raise RuntimeError( RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 51, in display run(session, cmd) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 90, in provider_save saver_info.save(session, path, **provider_kw) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 84, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 901, in save session.save(output, version=version, include_maps=include_maps) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 625, in save mgr.discovery(self._state_containers) File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at 0x0000020EA9223310>: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore ValueError: error processing: 'tasks' -> : Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore File "C:\Users\pb099337\Desktop\ChimeraX\bin\Lib\site- packages\chimerax\core\session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 Core Profile Context 22.20.26.08.221227 OpenGL renderer: AMD Radeon(TM) Graphics OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP EliteBook 845 14 inch G9 Notebook PC OS: Microsoft Windows 10 Enterprise (Build 19045) Memory: 16,442,728,448 MaxProcessMemory: 137,438,953,344 CPU: 12 AMD Ryzen 5 PRO 6650U with Radeon Graphics OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.0 Babel: 2.13.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.7.22 cftime: 1.6.2 charset-normalizer: 3.3.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.11.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.48.1 ChimeraX-AtomicLibrary: 10.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202310042257 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.11 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.32.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 comtypes: 1.1.14 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.12.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.0 filelock: 3.9.0 fonttools: 4.43.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.2 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.11.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.6 wcwidth: 0.2.8 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (2)
comment:1 by , 23 months ago
Component: | Unassigned → Sessions |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Unable to restore objects of NewerVersionQuery class |
comment:2 by , 23 months ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
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