Dead pseudobond group being saved in session

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.3.0-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 /Users/savannahbrown/Downloads/1h1d.pdb

1h1d.pdb title:  
Catechol O-methyltransferase [more info...]  
  
Chain information for 1h1d.pdb #1  
---  
Chain | Description  
A | catechol-O-methyltransferase  
  
Non-standard residues in 1h1d.pdb #1  
---  
BIA — 1-(3,4,dihydroxy-5-nitrophenyl)-3-{4-[3-(trifluoromethyl) phenyl]
piperazin-1-yl}propan-1-one (bia 3-335)  
MG — magnesium ion  
SAM — S-adenosylmethionine  
  

> delete solvent

> label @@display

> label delete :ligand

> label delete :BIA

> label delete :MG

> label delete :SAM

> open 1h1d

Summary of feedback from opening 1h1d fetched from pdb  
---  
notes | Fetching compressed mmCIF 1h1d from
http://files.rcsb.org/download/1h1d.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
Fetching CCD SAM from http://ligand-expo.rcsb.org/reports/S/SAM/SAM.cif  
Fetching CCD BIA from http://ligand-expo.rcsb.org/reports/B/BIA/BIA.cif  
  
1h1d title:  
Catechol O-Methyltransferase [more info...]  
  
Chain information for 1h1d #2  
---  
Chain | Description  
A | catechol-O-methyltransferase  
  
Non-standard residues in 1h1d #2  
---  
BIA — 1-(3,4,dihydroxy-5-nitrophenyl)-3-{4-[3-(trifluoromethyl) phenyl]
piperazin-1-yl}propan-1-one (bia 3-335)  
MG — magnesium ion  
SAM — S-adenosylmethionine  
  
  

> label delete

> close #2

> close #1

> open /Users/savannahbrown/Downloads/1h1d.pdb

1h1d.pdb title:  
Catechol O-methyltransferase [more info...]  
  
Chain information for 1h1d.pdb #1  
---  
Chain | Description  
A | catechol-O-methyltransferase  
  
Non-standard residues in 1h1d.pdb #1  
---  
BIA — 1-(3,4,dihydroxy-5-nitrophenyl)-3-{4-[3-(trifluoromethyl) phenyl]
piperazin-1-yl}propan-1-one (bia 3-335)  
MG — magnesium ion  
SAM — S-adenosylmethionine  
  

> delete solvent

> hbonds

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

240 hydrogen bonds found  

> hide hbonds

> hbonds :BIA

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

5 hydrogen bonds found  

> hbonds :MG

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

0 hydrogen bonds found  

> hbonds :BIA,MG,SAM

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

18 hydrogen bonds found  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color hbonds magenta

> hbonds showDist true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

240 hydrogen bonds found  

> undo

Undo failed, probably because structures have been modified.  

> close #1.1#1.2.1#1#1.2

> open /Users/savannahbrown/Downloads/1h1d.pdb

1h1d.pdb title:  
Catechol O-methyltransferase [more info...]  
  
Chain information for 1h1d.pdb #1  
---  
Chain | Description  
A | catechol-O-methyltransferase  
  
Non-standard residues in 1h1d.pdb #1  
---  
BIA — 1-(3,4,dihydroxy-5-nitrophenyl)-3-{4-[3-(trifluoromethyl) phenyl]
piperazin-1-yl}propan-1-one (bia 3-335)  
MG — magnesium ion  
SAM — S-adenosylmethionine  
  

> delete solvent

> hbonds :BIA,MG,SAM

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

18 hydrogen bonds found  

> hbonds :BIA,MG,SAM showDist true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A SER 216 N  

18 hydrogen bonds found  

> save session /Users/savannahbrown/Desktop/hbonds.cxs

Traceback (most recent call last):  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondGroup' object's 'name' property raised
AttributeError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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 'pb_dist_monitor' ->
<chimerax.dist_monitor.monitor.DistancesMonitor object at 0x11c106410> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x121ae28d0>: Execution of
'PseudobondGroup' object's 'name' property raised AttributeError  
  
RuntimeError: Error while saving session data for 'pb_dist_monitor' -> -> :
Execution of 'PseudobondGroup' object's 'name' property raised AttributeError  
  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondGroup' object's 'name' property raised
AttributeError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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 'pb_dist_monitor' ->
<chimerax.dist_monitor.monitor.DistancesMonitor object at 0x11c106410> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x121ae28d0>: Execution of
'PseudobondGroup' object's 'name' property raised AttributeError  
  
RuntimeError: Error while saving session data for 'pb_dist_monitor' -> -> :
Execution of 'PseudobondGroup' object's 'name' property raised AttributeError  
  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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/savannahbrown/Desktop/hbonds.cxs

Traceback (most recent call last):  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondGroup' object's 'name' property raised
AttributeError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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 'pb_dist_monitor' ->
<chimerax.dist_monitor.monitor.DistancesMonitor object at 0x11c106410> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x121ae28d0>: Execution of
'PseudobondGroup' object's 'name' property raised AttributeError  
  
RuntimeError: Error while saving session data for 'pb_dist_monitor' -> -> :
Execution of 'PseudobondGroup' object's 'name' property raised AttributeError  
  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot  
'category': self.name,  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondGroup' object's 'name' property raised
AttributeError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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 'pb_dist_monitor' ->
<chimerax.dist_monitor.monitor.DistancesMonitor object at 0x11c106410> ->
<chimerax.atomic.pbgroup.PseudobondGroup object at 0x121ae28d0>: Execution of
'PseudobondGroup' object's 'name' property raised AttributeError  
  
RuntimeError: Error while saving session data for 'pb_dist_monitor' -> -> :
Execution of 'PseudobondGroup' object's 'name' property raised AttributeError  
  
File
"/private/var/folders/1j/jkww_gg95bv1wpx0m9dk9j5m0000gn/T/AppTranslocation/5E962CD1-9297-4001-AB9A-25ECF595B4E2/d/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-14.4.23
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.

[Eric Pettersen]

To reproduce, have to start from the 'open' that's before the 'undo'.

[Eric Pettersen]

Fixed by other changes since the 0.91 release.