id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1698 Session save: No bundle information for chimerax.atomic.molobject.PseudobondManager j.r.lewandowski@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-08) Description I tried to save ChimeraX session. Before that I have renamed and changed IDs for a number of models in an existing PDB. Log: UCSF ChimeraX version: 0.9 (2019-02-08) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jozef/Documents/ScienceF/Warwick/Papers/Papers - published/2018 NPR review - transAT/pikromycin-PKS-module-cryoEM.pdb"" Summary of feedback from opening /Users/jozef/Documents/ScienceF/Warwick/Papers/Papers - published/2018 NPR review - transAT/pikromycin-PKS-module-cryoEM.pdb --- warnings | Cannot find LINK/SSBOND residue ALA (479 ) Cannot find LINK/SSBOND residue MSE (480 ) Cannot find LINK/SSBOND residue ALA (554 ) Cannot find LINK/SSBOND residue MSE (555 ) Cannot find LINK/SSBOND residue GLY (566 ) 140 messages similar to the above omitted Start residue of secondary structure not found: HELIX 1 1 GLU A 9 GLU A 39 1 31 Start residue of secondary structure not found: HELIX 2 2 SER A 56 GLY A 66 1 11 Start residue of secondary structure not found: HELIX 3 3 PRO A 75 GLY A 79 1 5 Start residue of secondary structure not found: HELIX 4 4 ALA A 100 GLY A 104 1 5 Start residue of secondary structure not found: HELIX 5 5 SER A 106 ALA A 131 1 26 1579 messages similar to the above omitted pikromycin-PKS-module-cryoEM.pdb title: Structure of the ketosynthase-acyltransferase didomain of module 5 from debs. [more info...] Chain information for pikromycin-PKS-module-cryoEM.pdb --- Chain | Description 1.1/A 1.1/B | DEBS 1.3/A 1.7/A 1.11/A 1.12/A 1.18/A 1.19/A 1.24/A 1.28/A | DEBS 1.4/A 1.5/A 1.13/A 1.14/A 1.20/A 1.21/A 1.25/A 1.26/A | DEBS 1.8/A 1.15/A 1.22/A 1.8/B 1.15/B 1.22/B | DEBS 1.2/B 1.6/B 1.9/B 1.10/B 1.16/B 1.17/B 1.23/B 1.27/B | DEBS > close #1.24-28 > hide #1.23 target m > hide #1.23 target m > close #1.23 > hide #1.22 target m > close #1.22 > hide #1.21 target m > close #1.21 > hide #!1.20 models > close #1.20 > hide #!1.19 models > close #1.19 > hide #1.18 target m > close #1.18 > hide #1.17 target m > close #1.17 > hide #1.16 target m > close #1.16 > hide #1.15 target m > close #1.15 > hide #1.14 target m > show #1.14 target m > hide #1.13 target m > hide #1.13 target m > show #1.13 target m > hide #1.12 target m > show #1.12 target m > hide #1.11 target m > show #1.11 target m > hide #1.10 target m > show #1.10 target m > hide #1.9 target m > show #1.9 target m > hide #1.8 target m > show #1.8 target m > hide #1.7 target m > show #1.7 target m > close #1.7 > hide #1.6 target m > close #1.6 > hide #1.5 target m > close #1.5 > hide #1.4 target m > close #1.4 > hide #1.3 target m > close #1.3 > hide #1.2 target m > close #1.2 > hide #1.1 target m > close #1.1 Developer warnings in user commands index: * didn't expect href to be to tools/sequenceviewer.html on line 246 > hide #!1.8 models > show #!1.8 models > hide #!1.8 models > show #!1.8 models > rename #1.8 KS id #1.1 > rename #1.8 KS id #1.1 > hide #!1.9 models > show #!1.9 models > hide #!1.9 models > show #!1.9 models > hide #!1.10 models > show #!1.10 models > hide #!1.9 models > show #!1.9 models > hide #!1.10 models > show #!1.10 models > rename #1.1 AT id #1.2 > rename #1.1 KS id #1.1 > rename #1.1 KS id #1.1 > rename #1.2 KS id #1.1 > rename #1.9 AT id #1.2 > hide #!1.10 models > show #!1.10 models > rename #1.10 AT id #1.3 > hide #!1.11 models > show #!1.11 models > rename #1.11 KR id #1.4 > hide #!1.12 models > show #!1.12 models > rename #1.12 KR id #1.5 > hide #!1.13 models > show #!1.13 models > hide #!1.14 models > show #!1.14 models > rename #1.13 ACP id #1.6 > rename #1.14 ACP id #1.7 > rename #1 pikromycin-module5-PKS > set bgColor white > save session /Users/jozef/Desktop/pikromycin-module5-PKS-from-cyoEM.cxs Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 810, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 573, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2615, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 916, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 224, in discovery uid = _UniqueName.from_obj(self.session, value) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) See log for complete Python traceback. > save session /Users/jozef/Desktop/pikromycin-module5-PKS.cxs Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 810, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 573, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2615, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 916, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 224, in discovery uid = _UniqueName.from_obj(self.session, value) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) See log for complete Python traceback. > save session /Users/jozef/Desktop/pikromycin_module5_PKS.cxs Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 810, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 573, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2615, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 916, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 224, in discovery uid = _UniqueName.from_obj(self.session, value) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) See log for complete Python traceback. > save session /Users/jozef/Desktop/pikromycinmodule5PKS.cxs Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 810, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 573, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2615, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 916, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 224, in discovery uid = _UniqueName.from_obj(self.session, value) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) See log for complete Python traceback. > save session /Users/jozef/Desktop/pikromycinmodule5PKS.cxs Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 810, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 573, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2615, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 916, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 224, in discovery uid = _UniqueName.from_obj(self.session, value) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) See log for complete Python traceback. > save session /Users/jozef/Desktop/pik.cxs Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 810, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 573, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 141, in display fmt.save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 40, in save return self._save(session, filename) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 93, in _session_save run(session, ""save session %s"" % quote_if_necessary(filename)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2615, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 916, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 203, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 730, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 497, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 224, in discovery uid = _UniqueName.from_obj(self.session, value) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager RuntimeError: No bundle information for chimerax.atomic.molobject.PseudobondManager File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 128, in from_obj obj_cls.__module__, obj_cls.__name__)) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-12.0.21 355.11.10.50.10.103 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed major Sessions fixed chimera-programmers Elaine Meng all ChimeraX