Opened 6 years ago

Closed 6 years ago

#2407 closed defect (fixed)

Problem saving session involving Clipper

Reported by: coutandin@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-10)
Description
(Describe the actions that caused this problem to occur here)

Log:
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 293, in _run_startup_commands  
run(self.session, cmd_text)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2662, in run  
raise UserError(self._error)  
chimerax.core.errors.UserError: Expected a keyword  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 295, in _run_startup_commands  
session.logger.status(str(err), color="crimson")  
NameError: name 'session' is not defined  
  
Error processing trigger "ready":  
NameError: name 'session' is not defined  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 295, in _run_startup_commands  
session.logger.status(str(err), color="crimson")  
  
See log for complete Python traceback.  
  
UCSF ChimeraX version: 0.91 (2019-09-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/daniel/phenix/G040_1_ALL/Autosharpen_2/sharpened_map.ccp4

Opened sharpened_map.ccp4, grid size 280,280,280, pixel 0.837, shown at level
3.5, step 2, values float32  

> open /Users/daniel/phenix/G040_1_ALL/ISOLE_190913/010.cif

Summary of feedback from opening
/Users/daniel/phenix/G040_1_ALL/ISOLE_190913/010.cif  
---  
warnings | Unknown polymer entity '1' near line 157  
Unknown polymer entity '2' near line 10585  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 010.cif #2  
---  
Chain | Description  
A | ?  
B | ?  
  

> transparency 50

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for 010.cif  
---  
Chain | Description  
2.3/A | ?  
2.3/B | ?  
  
Done loading forcefield  

> select #2 /A :219

22 atoms, 21 bonds, 1 model selected  

> view sel

> select #2 /A :276

21 atoms, 21 bonds, 1 model selected  

> view sel

> view sel

> view sel

> view sel

> select clear

> select #2 /A :272-281

177 atoms, 177 bonds, 1 model selected  
Loading residue template for ATP from internal database  
Bad residue number: match  
Excluding residue  
Bad residue number: 87  
Excluding residue  

> select #2 /A :272-281

177 atoms, 177 bonds, 1 model selected  

> view sel

> select clear

> select #2 /A :275

22 atoms, 21 bonds, 1 model selected  

> view sel

> view sel

> view sel

> view sel

> view sel

Not saving entity_poly_seq for non-authoritative sequences  

Unable to flip peptide bond after 50 rounds. Giving up.  

> view sel

> view sel

> view sel

> select clear

Not saving entity_poly_seq for non-authoritative sequences  

> view sel

> view sel

> view sel

Not saving entity_poly_seq for non-authoritative sequences  

> select clear

> view sel

> view sel

Not saving entity_poly_seq for non-authoritative sequences  

> view sel

> view sel

Not saving entity_poly_seq for non-authoritative sequences  

> view sel

> view sel

> view sel

> select clear

> view sel

> view sel

> view sel

> view sel

> view sel

> view sel

Not saving entity_poly_seq for non-authoritative sequences  

> save session /Users/daniel/phenix/G040_1_ALL/ISOLE_190913/016.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 288, in process  
return copy_state(data, convert=convert)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 199, in copy_state  
return _copy(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 197, in _copy  
return convert(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 287, in convert  
return add_obj(obj, parents)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 871, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 138, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1089, in save  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2691, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 981, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 288, in process  
return copy_state(data, convert=convert)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 199, in copy_state  
return _copy(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 186, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 197, in _copy  
return convert(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 287, in convert  
return add_obj(obj, parents)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
RuntimeError: Unable to restore objects of Symmetry_Manager class in ChimeraX-
Clipper bundle because the class name is not listed in the name to class table
for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem saving session involving Clipper

Reported by Daniel Coutandin

in reply to:  2 ; comment:2 by Tristan Croll, 6 years ago 

Yep - coming to grips with the ChimeraX session save/restore framework is near the top of my to-do list, but right now neither Clipper nor ISOLDE work with it. Sorry for the trouble!

comment:3 by Tristan Croll, 6 years ago

Resolution: → fixed
Status: assigned → closed

Session save/restore is now all working in my builds, and will be released in ISOLDE 1.0b4 as soon as the official stable release of ChimeraX 0.91 goes live.

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