Nucleotides trying to save closed structure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
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
> /Volumes/My_Book/Leishmania_RNA_virus/RESULTS/Docking_cap/Docking_by_Vacha/figures_preparation_Francesco/top2000/top2000.cxs

opened ChimeraX session  

> show #3 models

> hide #!1 models

> view

> view orient

> show #3 atoms

> close #3

> open
> /Volumes/My_Book/Leishmania_RNA_virus/RESULTS/Docking_cap/Docking_by_Vacha/figures_preparation_Francesco/top2000/cap4_docked_top2000.pdb

Summary of feedback from opening
/Volumes/My_Book/Leishmania_RNA_virus/RESULTS/Docking_cap/Docking_by_Vacha/figures_preparation_Francesco/top2000/cap4_docked_top2000.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Ligand: lig_5e7929050da23.pdb  
  
Ignored bad PDB record found on line 123  
REMARK Ligand: lig_5e7929050da23.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 245  
REMARK Ligand: lig_5e7902f9ea4a3.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 367  
REMARK Ligand: lig_5c939b60274e7.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 489  
REMARK Ligand: lig_5e7903620352c.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 611  
REMARK Ligand: lig_5e750206a5634.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 733  
REMARK Ligand: lig_5e79035096c1a.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 855  
REMARK Ligand: lig_5e7502ae8fcb5.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 977  
REMARK Ligand: lig_5e7903620352c.pdb  
  

[many silmilar blocks deleted]
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238145  
REMARK Ligand: lig_5e75017c7a4c9.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238267  
REMARK Ligand: lig_5e7902a564e53.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238389  
REMARK Ligand: lig_5e7903620352c.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238511  
REMARK Ligand: lig_5e7903c38ac78.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238633  
REMARK Ligand: lig_5e75025a621bc.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238755  
REMARK Ligand: lig_5c939b457d83d.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238877  
REMARK Ligand: lig_5e79032db0262.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 238999  
REMARK Ligand: lig_5e792921e8342.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239121  
REMARK Ligand: lig_5e7902960a7b3.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239243  
REMARK Ligand: lig_5e7903f823598.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239365  
REMARK Ligand: lig_5e7928f732834.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239487  
REMARK Ligand: lig_5e79045e9ea02.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239609  
REMARK Ligand: lig_5e7502227991f.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239731  
REMARK Ligand: lig_5e75025a621bc.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239853  
REMARK Ligand: lig_5e7903d578f6d.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 239975  
REMARK Ligand: lig_5e79042c3cd37.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240097  
REMARK Ligand: lig_5e750206a5634.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240219  
REMARK Ligand: lig_5e7929752cee3.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240341  
REMARK Ligand: lig_5e7929675034e.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240463  
REMARK Ligand: lig_5e75029276619.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240585  
REMARK Ligand: lig_5e7501c1ba521.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240707  
REMARK Ligand: lig_5e7502ae8fcb5.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240829  
REMARK Ligand: lig_5e7903d578f6d.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 240951  
REMARK Ligand: lig_5c939b7b21344.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241073  
REMARK Ligand: lig_5e7502a0a6b72.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241195  
REMARK Ligand: lig_5e79035096c1a.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241317  
REMARK Ligand: lig_5e7501b3be71b.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241439  
REMARK Ligand: lig_5e792a2bafe3c.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241561  
REMARK Ligand: lig_5e7501eae637c.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241683  
REMARK Ligand: lig_5e750206a5634.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241805  
REMARK Ligand: lig_5e7502307c98a.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 241927  
REMARK Ligand: lig_5e7903f823598.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242049  
REMARK Ligand: lig_5e792921e8342.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242171  
REMARK Ligand: lig_5e7501b3be71b.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242293  
REMARK Ligand: lig_5e79032db0262.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242415  
REMARK Ligand: lig_5e7902e7c6195.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242537  
REMARK Ligand: lig_5c939adc20b42.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
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115 messages similar to the above omitted  
Ignored bad PDB record found on line 242659  
REMARK Ligand: lig_5e75024c5975b.pdb  
  
Duplicate atom serial number found: 1  
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Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242781  
REMARK Ligand: lig_5e79298339366.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
Ignored bad PDB record found on line 242903  
REMARK Ligand: lig_5e79030c29453.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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115 messages similar to the above omitted  
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REMARK Ligand: lig_5e7502307c98a.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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115 messages similar to the above omitted  
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REMARK Ligand: lig_5e7928b1d5da5.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
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115 messages similar to the above omitted  
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REMARK Ligand: lig_5c939b95e2aac.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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115 messages similar to the above omitted  
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REMARK Ligand: lig_5e7903f823598.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
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115 messages similar to the above omitted  
Ignored bad PDB record found on line 243513  
REMARK Ligand: lig_5e79045e9ea02.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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115 messages similar to the above omitted  
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REMARK Ligand: lig_5e75024c5975b.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
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115 messages similar to the above omitted  
Ignored bad PDB record found on line 243757  
REMARK Ligand: lig_5e7903b287524.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
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115 messages similar to the above omitted  
Ignored bad PDB record found on line 243879  
REMARK Ligand: lig_5e7928f732834.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
115 messages similar to the above omitted  
  
Chain information for cap4_docked_top2000.pdb #3  
---  
Chain | Description  
| No description available  
  

> show #!2 models

> save session
> /Volumes/My_Book/Leishmania_RNA_virus/RESULTS/Docking_cap/Docking_by_Vacha/figures_preparation_Francesco/top2000/top2000.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' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x157dfbf10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x12e0fe410>
'cap4_docked_top2000.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'cap4_docked_top2000.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 <lambda>  
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' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x157dfbf10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x12e0fe410>
'cap4_docked_top2000.pdb': 'NoneType' object has no attribute 'array'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'cap4_docked_top2000.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 INTEL-10.36.26
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Greg Couch]

Duplicate of #2955. Finally able to reproduce and fix.