Opened 6 years ago

Closed 6 years ago

#2508 closed defect (fixed)

atomic structure session save: 'utf-8' codec can't decode byte: invalid start byte

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Sessions 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 (2019-06-21)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-06-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/hecklersyrine/Desktop/TR__PDB_importants/PPAR_LBD_F310S_PF26_T007_refine_078.pdb

Summary of feedback from opening
/Users/hecklersyrine/Desktop/TR__PDB_importants/PPAR_LBD_F310S_PF26_T007_refine_078.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-10-04 Time 17:36:12 Paris, Madrid (heure d??t?) +0200
(1570203372.59 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : L:\bejis\Crystallography\PPAR_LBD_F310_PF26_T007\Dernier
affinement Natacha\F310S_refine_051.mtz  
  
65 messages similar to the above omitted  
  
Chain information for PPAR_LBD_F310S_PF26_T007_refine_078.pdb #1  
---  
Chain | Description  
A | No description available  
C | No description available  
  

> open "/Users/hecklersyrine/Desktop/TR__PDB_importants/6fzp PPAR WT LBD
GW1929 PGC1a.pse"

Unrecognized file suffix '.pse'  
Unrecognized file suffix '.pse'  

> open /Users/hecklersyrine/Desktop/TR__PDB_importants/6fzp.pdb

6fzp.pdb title:  
Ppar γ complex [more info...]  
  
Chain information for 6fzp.pdb #2  
---  
Chain | Description  
A | peroxisome proliferator-activated receptor γ  
C | peroxisome proliferator-activated receptor γ coactivator 1-α  
  
Non-standard residues in 6fzp.pdb #2  
---  
EDK —
(2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic
acid  
NA — sodium ion  
  

> open /Users/hecklersyrine/Desktop/TR__PDB_importants/6fzj.pdb

6fzj.pdb title:  
Ppar γ mutant complex [more info...]  
  
Chain information for 6fzj.pdb #3  
---  
Chain | Description  
A B | peroxisome proliferator-activated receptor γ  
C D | peroxisome proliferator-activated receptor γ coactivator 1-α  
  
Non-standard residues in 6fzj.pdb #3  
---  
CL — chloride ion  
EDK —
(2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic
acid  
IOD — iodide ion  
  

> mmaker #1 to #2 #3 showAlignment true

Specify a single 'to' model only  

> mmaker #1 to #2 to #3 showAlignment true

Repeated keyword argument "to"  

> mmaker #1 to #2 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6fzp.pdb, chain A (#2) with
PPAR_LBD_F310S_PF26_T007_refine_078.pdb, chain A (#1), sequence alignment
score = 1213.3  
Alignment identifier is 1  
2 headers  
RMSD between 219 pruned atom pairs is 0.719 angstroms; (across all 250 pairs:
5.536)  
  

> mmaker #1 to #3 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6fzj.pdb, chain B (#3) with
PPAR_LBD_F310S_PF26_T007_refine_078.pdb, chain A (#1), sequence alignment
score = 1233.9  
Alignment identifier is 2  
2 headers  
RMSD between 220 pruned atom pairs is 0.691 angstroms; (across all 255 pairs:
5.500)  
  

> mmaker #2 to #3 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6fzj.pdb, chain B (#3) with 6fzp.pdb, chain A (#2), sequence
alignment score = 1339  
Alignment identifier is 3  
2 headers  
RMSD between 258 pruned atom pairs is 0.420 angstroms; (across all 258 pairs:
0.420)  
  

> select #1

2246 atoms, 2203 bonds, 1 pseudobond, 2 models selected  

> select #2

2226 atoms, 2211 bonds, 6 pseudobonds, 3 models selected  

> select #3

4959 atoms, 4632 bonds, 2 pseudobonds, 2 models selected  

> ~select #3

Nothing selected  

> set bgColor white

> select #3

4959 atoms, 4632 bonds, 2 pseudobonds, 2 models selected  

> select #3

4959 atoms, 4632 bonds, 2 pseudobonds, 2 models selected  

> ~select #3

Nothing selected  

> select #3

4959 atoms, 4632 bonds, 2 pseudobonds, 2 models selected  

> save session "/Users/hecklersyrine/Desktop/TR__PDB_importants/F310-6FZP-6FZJ
align.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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/session.py", line 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 84, in handle_scheme  
cmd(self.session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 148, in _file_save  
session.ui.main_window.file_save_cb(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 595, 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 1058, 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 2641, 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 952, 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 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> ~select #3

Nothing selected  

> lighting full

> lighting soft

> show #3 target m

> save session "/Users/hecklersyrine/Desktop/TR__PDB_importants/F310-6FZP-6FZJ
align.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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/session.py", line 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/ui/gui.py", line 855, 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 595, 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 1058, 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 2641, 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 952, 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 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session "/Users/hecklersyrine/Desktop/TR__PDB_importants/F310_6FZP_6FZJ
align.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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/session.py", line 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 84, in handle_scheme  
cmd(self.session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 148, in _file_save  
session.ui.main_window.file_save_cb(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 595, 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 1058, 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 2641, 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 952, 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 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 84, in handle_scheme  
cmd(self.session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 148, in _file_save  
session.ui.main_window.file_save_cb(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 595, 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/map/savemap.py", line 52, in save  
self._map_menu.value.id_string)  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/savemap.py", line 52, in save  
self._map_menu.value.id_string)  
  
See log for complete Python traceback.  
  

> save session "/Users/hecklersyrine/Desktop/F310_6FZP_6FZJ align.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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/session.py", line 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 84, in handle_scheme  
cmd(self.session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 148, in _file_save  
session.ui.main_window.file_save_cb(session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 595, 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 1058, 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 2641, 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 952, 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 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session "/Users/hecklersyrine/Desktop/F310_6FZP_6FZJ align.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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/session.py", line 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/ui/gui.py", line 855, 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 595, 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 1058, 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 2641, 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 952, 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 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session "/Users/hecklersyrine/Desktop/F310 6FZP 6FZJ align.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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/session.py", line 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
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/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2407, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 165, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1628, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x92 in position 59:
invalid start byte  
  
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/ui/gui.py", line 855, 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 595, 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 1058, 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 2641, 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 952, 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 765, 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 534, 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 234, in discovery  
self.processed[key] = self.process(obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'utf-8' codec can't decode byte
0x92 in position 59: invalid start byte  
  
RuntimeError: Error while saving session data for "": 'utf-8' codec can't
decode byte 0x92 in position 59: invalid start byte  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 450 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (3)

comment:1 by pett, 6 years ago

Component: Unassigned → Sessions
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → atomic structure session save: 'utf-8' codec can't decode byte: invalid start byte

comment:2 by pett, 6 years ago

Possibly due to non-ASCII in REMARK records?

comment:3 by pett, 6 years ago

Resolution: → fixed
Status: accepted → closed

Changed cchar_to_pystring() [used when forming session-save data] to replace bad characters instead of throwing error

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