Opened 7 years ago

Closed 6 years ago

#1698 closed defect (fixed)

Session save: No bundle information for chimerax.atomic.molobject.PseudobondManager

Reported by: j.r.lewandowski@… Owned by: Greg Couch
Priority: major Milestone:
Component: Sessions Version:
Keywords: Cc: chimera-programmers, Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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 <lambda>  
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

Change History (9)

comment:1 by Eric Pettersen, 7 years ago

Cc: chimera-programmers Elaine Meng added
Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session save: No bundle information for chimerax.atomic.molobject.PseudobondManager

Reported by Jozef Lewandowski

Easy to reproduce: open any structure with pseudobonds (e.g. 2gbp) and save a session.

comment:2 by Eric Pettersen, 7 years ago

Priority: normal → major

comment:3 by Greg Couch, 7 years ago

Status: assigned → accepted

Works with 2gbp for me. But can reproduce with:

open 1a0m
hbonds
save foo.cxs

comment:4 by Greg Couch, 7 years ago

The list of files for the ChimeraX-Atomic is wrong in the daily build. That list of files is used to discover which bundle a module is in. For some, as yet unknown reason, the files listed in site-packages/ChimeraX_Atomic-1.0.dist-info/RECORD are:

ChimeraX_Atomic-1.0.data/purelib/chimerax/atomic/__init__.py,sha256=SJIWS1ipSCiRHvnymfIM8CNuiscdmztHz11-3dCDozU,4471

instead of:

chimerax/atomic/__init__.py,sha256=SJIWS1ipSCiRHvnymfIM8CNuiscdmztHz11-3dCDozU,4471

And there are other packages that have an extra .data/purelib in the recorded installed file names -- ChimeraX_AlignmentHdrs, ChimeraX_SpaceNavigator, and ChimeraX_Test.

This bug does not happen on my development machine.

in reply to:  5 ; comment:5 by Eric Pettersen, 7 years ago 

Those packages have compiled components.

comment:6 by Greg Couch, 7 years ago

It's a bug with the latest version of pip. 19.0.2 creates the buggy RECORD files and 19.0.1 works.

comment:7 by Greg Couch, 7 years ago

Owner: changed from Greg Couch to Conrad Huang
Status: accepted → assigned

Workaround is in place. This is probably an interaction between bundle_builder and the new pip, so handing it off to Conrad for now.

comment:8 by Conrad Huang, 6 years ago

Owner: changed from Conrad Huang to Greg Couch

We're at pip 19.1.1 and RECORD shows the correct name. What was the workaround? Using 19.0.1? If so, please close this ticket since 19.1.1 seems to work correctly again.

comment:9 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed upstream.

Note: See TracTickets for help on using tickets.