id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2988 Session save: 'NoneType' object has no attribute 'array' Fengwei.Zheng@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warnings | No presets found in custom preset folder /Users/fengwei.zheng/Documents/Draft_PolD/Figure No presets found in custom preset folder /Users/fengwei.zheng/Documents/Draft_PolD/Session UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2b_ystPolDcmplx- > Pol.cxs format session opened ChimeraX session Expected an objects specifier or a keyword > close #2 > name PIP #1/A:997-1003 > select PIP :< 4.5 & #1 & ~PIP 138 atoms, 134 bonds, 1 model selected > show sel cartoons > view sel > select PIP :< 4.5 & #1 187 atoms, 183 bonds, 1 model selected > show sel cartoons > mlp sel Map values for surface ""409-ystPolDcplx_156-679.pdb_H SES surface"": minimum -28.01, mean -5.135, maximum 24.3 Map values for surface ""409-ystPolDcplx_156-679.pdb_A SES surface"": minimum -29.35, mean -4.544, maximum 25.07 > undo > select PIP :< 4.5 & #1 & ~PIP 138 atoms, 134 bonds, 1 model selected Expected an atoms specifier or a keyword Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword Unknown command: ~mlp > hide surfaces > select PIP :< 4.5 & #1 & ~PIP 138 atoms, 134 bonds, 1 model selected > mlp sel Map values for surface ""409-ystPolDcplx_156-679.pdb_H SES surface"": minimum -28.01, mean -5.135, maximum 24.3 Map values for surface ""409-ystPolDcplx_156-679.pdb_A SES surface"": minimum -29.35, mean -4.544, maximum 25.07 > close session > open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-PCNA.cxs > format session opened ChimeraX session > hide surfaces > select PIP :< 4.5 & #1 & ~PIP 138 atoms, 134 bonds, 1 model selected > mlp sel Map values for surface ""409-ystPolDcplx_156-679.pdb_H SES surface"": minimum -28.01, mean -5.135, maximum 24.3 Map values for surface ""409-ystPolDcplx_156-679.pdb_A SES surface"": minimum -29.35, mean -4.544, maximum 25.07 > hide sel > hide surfaces > select up 140 atoms, 134 bonds, 3 models selected > select PIP :< 4.5 & #1 187 atoms, 183 bonds, 1 model selected > open /Users/fengwei.zheng/Documents/Structures/PolD/cryosparc_P3_J409.mrc Opened cryosparc_P3_J409.mrc, grid size 420,420,420, pixel 0.826, shown at level 0.0788, step 2, values float32 > volume #5 step 1 > volume #5 level 0.25 > volume zone #5 nearAtoms sel range 2 > volume #6 style mesh > volume #6 color gold > graphics silhouettes false > undo > undo > redo > redo > redo No redo action is available > show sel atoms > style sel stick Changed 187 atom styles > hide sel cartoons > hide cartoons > volume #6 level 0.2 > volume #6 level 0.1 > volume #6 level 0.15 Missing or invalid ""surfaces"" argument: invalid surfaces specifier Missing or invalid ""surfaces"" argument: invalid surfaces specifier Missing or invalid ""surfaces"" argument: empty atom specifier Missing or invalid ""surfaces"" argument: empty atom specifier > surface dust #1 size 5 > undo > open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2a_ystPolDcmplx- > Exo.cxs format session opened ChimeraX session > open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2b_ystPolDcmplx- > Pol.cxs format session opened ChimeraX session > open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP-PCNA.cxs > format session opened ChimeraX session > hide surfaces > name PIP #1/a:997-1003 > name PIP #1/a:997-1003 > select PIP :< 4.5 & #1 187 atoms, 183 bonds, 1 model selected > open /Users/fengwei.zheng/Documents/Structures/PolD/cryosparc_P3_J409.mrc Opened cryosparc_P3_J409.mrc, grid size 420,420,420, pixel 0.826, shown at level 0.0788, step 2, values float32 > volume #5 level 0.15 > surface dust #5 size 5 > volume #5 step 1 > surface dust #5 size 5 > surface dust #5 size 5 > volume zone #5 nearAtoms sel range 2 > volume #6 style mesh > hide cartoons > surface dust #6 > select PIP :< 4.5 & #1 187 atoms, 183 bonds, 1 model selected > show sel atoms > style sel stick Changed 187 atom styles > volume #6 color peru > graphics silhouettes false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > select clear > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes true > graphics silhouettes false > lighting simple > lighting full > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > lighting soft > lighting soft > lighting simple > volume #6 level 0.2 > volume #6 level 0.25 > hide #1/H atoms > close #6 Expected an objects specifier or a keyword > select @display Nothing selected > select @@display 1938 atoms, 2095 bonds, 3 models selected > hide #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!1 models > select #4 8154 atoms, 7804 bonds, 28 pseudobonds, 3 models selected > ~select #4 Nothing selected > close #4 > close #3 > close #2 > select @@display 97 atoms, 95 bonds, 1 model selected > volume zone #5 nearAtoms sel range 2 > surface dust #2 > volume #2 level 0.25 > volume #2 style mesh > select clear > select /A:992@C 1 atom, 1 model selected > select up 7 atoms, 6 bonds, 2 models selected > select up 138 atoms, 138 bonds, 2 models selected > select clear > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 7 atoms, 6 bonds, 2 models selected > select up 138 atoms, 138 bonds, 2 models selected > select clear > hide #1/992-993 > hide #1/992-993 atoms > hide #1/A:992-993 > close #2 > undo > redo > select @@disp 16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected > hide cartoons > select @@disp 16769 atoms, 17166 bonds, 42 pseudobonds, 3 models selected > select clear > select /A:1104@ZN 1 atom, 1 model selected > hide ions > volume zone #5 nearAtoms sel range 2 > surface dust #2 > volume #2 style mesh > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.35 > volume #2 level 0.3 > volume #2 level 0.25 > volume #2 level 0.2 > select clear > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > color #2 #cd853f > save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP- > mesh.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 911, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 641, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 139, in display fmt.save(session, filename) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 1100, in save run(session, cmd) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 992, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. > save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP- > mesh.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 911, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 641, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 139, in display fmt.save(session, filename) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 1100, in save run(session, cmd) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 992, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. > save session /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP- > mesh.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 911, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 641, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 139, in display fmt.save(session, filename) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 1100, in save run(session, cmd) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 992, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. > save session > /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig2e_PIP_mesh.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 276, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2391, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 159, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 325, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 911, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 641, in file_save_cb self.save_dialog.display(self, session) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 139, in display fmt.save(session, filename) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 1100, in save run(session, cmd) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 992, in save_session save(session, filename, **kw) File ""/Applications/ChimeraX-0.91.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-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for 'nucleotides' -> -> '409-humPolDcplx.pdb': 'NoneType' object has no attribute 'array' File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 279, in process raise RuntimeError(msg) See log for complete Python traceback. OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Sessions duplicate all ChimeraX