Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2325 closed defect (fixed)

2D labels: session save: LabelModel class not found; also some visibility problems

Reported by: papai@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-13)
Description
I tried to save the session. Before that I had problems with the visibility of 2D labels.

Log:
> mousemode rightmode zoom

> toolshed show "side view"

UCSF ChimeraX version: 0.91 (2019-08-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/SAGA-5-6.pdb
/Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-taf5WD.pdb
/Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-taf5-6b.pdb
/Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-taf5-6a.pdb

  
  
  
  
Chain information for SAGA-5-6.pdb #1.1  
---  
Chain | Description  
M | No description available  
N | No description available  
  
Chain information for 2d-taf5WD.pdb #1.2  
---  
Chain | Description  
M | No description available  
  
Chain information for 2d-taf5-6b.pdb #1.3  
---  
Chain | Description  
C | No description available  
D | No description available  
  
Chain information for 2d-taf5-6a.pdb #1.4  
---  
Chain | Description  
B | No description available  
E | No description available  
  

> cartoon style #1 modeHelix tube radius 2.6 thickness 1.0 xsection oval sides
24

> help help:user

> hide #!1.4 models

> show #!1.4 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.4 models

> show #!1.4 models

> morph #1.4,1.1 frames 25

Require at least 2 structures for morph  

> close session

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-taf5WD.pdb

Chain information for 2d-taf5WD.pdb #1  
---  
Chain | Description  
M | No description available  
  

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-taf5-6a.pdb

Chain information for 2d-taf5-6a.pdb #2  
---  
Chain | Description  
B | No description available  
E | No description available  
  

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-taf5-6b.pdb

Chain information for 2d-taf5-6b.pdb #3  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/SAGA-5-6.pdb

Chain information for SAGA-5-6.pdb #4  
---  
Chain | Description  
M | No description available  
N | No description available  
  

> hide #!1 models

> show #!1 models

> morph #2,4 frames 25

Computed 26 frame morph #5  

> coordset #5 1,26

> close #5

> show #!2 models

> show #!4 models

> view list

No named views.  

> view

> view name egy

> view name two

> view egy

> perframe "view two" frames 20

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> view egy

> movie record supersample 3

> perframe "view two" frames 25

> wait 25

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-1.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-1.mp4  
  
executed try.cxc  

> cartoon style #1-4 modeHelix tube radius 2.6 thickness 0.7 xsection oval
sides 24

> morph #2,4 frames 25

Computed 26 frame morph #5  

> coordset #5 1,26

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!4 models

> view

> view list

Named views: egy, two  

> view egy

> view two 20

> close #5

> show #!2 models

> hide #!1 models

> show #!1 models

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

> color #4/N dodgerblue

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

> color #4/M steelblue

> color #4/M #000080

> color #4/M darkslateblue

> hide #!1 models

> show #!1 models

> hide #!3 models

> morph #2,4 frames 25

Computed 26 frame morph #5  

> coordset #5 1,26

> close #5

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> morph #2,4 frames 25

Computed 26 frame morph #5  

> coordset #5 1,26

> coordset #5 1,26 computeSs true

> coordset #5 1

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!3 models

> hide #!3 models

> view name two

> show #!3 models

> color #2/E darkolivegreen

> color #2/B forestgreen

> color #1/M forestgreen

> show #!4 models

> hide #!4 models

> color #3 #b22222

> select clear

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting soft

> view name egy

> perframe "transparency #3 100" frames 10

> perframe "transparency #3 100 target c" frames 10

> perframe "transparency #3 0 target c" frames 10

> perframe "transparency #3 100 target c" frames 100

> perframe "transparency #3 0 target c" frames 100

> hide #3

> hide #3 target c

> show #3 target c

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> close #5

> morph #2,4 frames 25

Computed 26 frame morph #5  

> coordset #5 1,26

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> view two

> show #!4 models

> hide #!3 models

> view name two

> view egy

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!3 models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide all target c

> show #1-3 target c

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> view egy

> movie record supersample 3

> view two 25

> wait 25

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-1.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-1.mp4  
  
executed try.cxc  

> show #!5 models

> show #5 target c

> show #!4 models

> show #!5 models

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> view egy

> movie record supersample 3

> view two 25

> wait 25

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-1.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-1.mp4  
  
executed try.cxc  

> view egy

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> view egy

> movie record supersample 3

> view two 25

> wait 25

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-2.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-2.mp4  
  
executed try.cxc  

> view egy

> hide all target c

> show #1-3 target c

> 2dlabels text TFIID

Expected a keyword  

Expected a keyword  

> 2dlabels delete #6

> 2dlabels text TFIID size 30 font helvetica bold true

> ui mousemode rightMode "move label"

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

> ui mousemode rightMode "move label"

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

> ui mousemode rightMode label

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> label delete residues

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode label

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

> ui mousemode rightMode "move label"

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

> 2dlabels delete #6

> ui mousemode rightMode zoom

> 2dlabels text TFIID size 30 xpos 100 ypos 100 font helvetica bold true

> 2dlabels delete #6

> 2dlabels text TFIID size 30 xpos 1 ypos 1 font helvetica bold true

> view egy

> 2dlabels delete #6

> 2dlabels text TFIID size 30 font helvetica bold true

> select #6

2 models selected  

> ui mousemode rightMode "translate selected models"

> toolshed show "Side View"

> close #6

> 2dlabels text TFIID size 30 font helvetica bold true

> select #6

2 models selected  

> ui mousemode rightMode "translate selected models"

> ~select #6

Nothing selected  

> 2dlabels text SAGA size 30 font helvetica bold true

> close #6

> 2dlabels text TFIID size 30 font helvetica bold true

> 2dlabels #7 text SAGA size 30 font helvetica bold true

> close #6

> ui mousemode rightMode zoom

> 2dlabels text TFIID size 30 font helvetica bold true

> ui mousemode rightMode "move label"

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

Missing or invalid "labels" argument: Expected 'all' or a 2d label name or a
label models specifier  

> select #6

2 models selected  

> ui mousemode rightMode "translate selected models"

> 2dlabels #6 text SAGA size 30 font helvetica bold true

> 2dlabels #6 text TFIID size 30 font helvetica bold true

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> view egy

> movie record supersample 3

> view two 35

> wait 35

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true pauseFrames 2

> wait 26

> 2dlabels #6 text SAGA size 30 font helvetica bold true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-3.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-3.mp4  
  
executed try.cxc  

> ui mousemode rightMode "translate selected models"

> view egy

> hide all target c

> show #1-3 target c

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show all target c

> view two

> 2dlabels #6 text TFIID size 30 font helvetica bold true

> view egy

> hide #4,5 target c

> ui mousemode rightMode zoom

> ui mousemode rightMode zoom

> 2dlabels text SAGA size 30 font helvetica bold true

> hide #!6.2 models

> 2dlabels text "Taf6 HEAT" size 30 font helvetica

> select #6

4 models selected  

> ~select #6

Nothing selected  

> select #6.3

1 model selected  

> ui mousemode rightMode "translate selected models"

> 2dlabels text "Taf6 HEAT (2)" size 30 font helvetica

> ~select #6.3

Nothing selected  

> select #6.4

1 model selected  

> ~select #6.4

Nothing selected  

> 2dlabels text "Taf5 NTD" size 30 font helvetica

> select #6.5

1 model selected  

> close #6.3-5

> close #6.2

> view egy

> view name egy

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> view egy

> movie record supersample 3

> view two 35

> wait 35

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true pauseFrames 2

> wait 26

> 2dlabels #6 text SAGA size 30 font helvetica bold true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-3.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-3.mp4  
  
executed try.cxc  

> cartoon style #5 modeHelix tube radius 2.6 thickness 0.7 xsection oval sides
24

> view egy

> hide #4,5 target c

> show #1-3 target c

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> view egy

> movie record supersample 3

> view two 35

> wait 35

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true pauseFrames 2

> wait 26

> 2dlabels #6 text SAGA size 30 font helvetica bold true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-4.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-4.mp4  
  
executed try.cxc  

> 2dlabels #6 text TFIID size 30 font helvetica bold true

> view egy

> hide #4,5 target c

> show #1-3 target c

> open /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try.cxc

> hide all target c

> show #1-3 target c

> 2dlabels #6 text TFIID size 30 font helvetica bold true

> view egy

> movie record supersample 3

> view two 35

> wait 35

> hide #3 target c

> wait 5

> hide #2 target c

> show #5 target c

> coordset #5 1,26 computeSs true pauseFrames 2

> wait 26

> 2dlabels #6 text SAGA size 30 font helvetica bold true

> wait 26

> show #4 target c

> hide #5,1 target c

> wait 5

> movie encode output /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/try-4.mp4 format h264 quality high framerate 25

Movie saved to /Users/gabor/.../For_Patrick/try-4.mp4  
  
executed try.cxc  

> view egy

> show #1-3 target c

> save session /Users/gabor/work/conferences/CSHL-
transcription-2019/For_Patrick/2d-saga_morph.cxs

Traceback (most recent call last):  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 264, in process  
return copy_state(data, convert=self._add_obj)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 174, in copy_state  
return _copy(data)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 172, in _copy  
return convert(data)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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 LabelModel class in ChimeraX-Label
bundle because the class name is not listed in the name to class table for
session restore  
  
RuntimeError: Unable to restore objects of LabelModel class in ChimeraX-Label
bundle because the class name is not listed in the name to class table for
session restore  
  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1062, in save  
run(session, cmd)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 956, in save_session  
save(session, filename, **kw)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 264, in process  
return copy_state(data, convert=self._add_obj)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 174, in copy_state  
return _copy(data)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 172, in _copy  
return convert(data)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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 LabelModel class in ChimeraX-Label
bundle because the class name is not listed in the name to class table for
session restore  
  
RuntimeError: Unable to restore objects of LabelModel class in ChimeraX-Label
bundle because the class name is not listed in the name to class table for
session restore  
  
File
"/Users/gabor/Chimera/ChimeraX_Daily-130819.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-1.68.22
OpenGL renderer: AMD Radeon HD 6770M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (3)

comment:1 by pett, 6 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 2D labels: session save: LabelModel class not found; also some visibility problems

Reported by Gabor Papai

comment:2 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

The error saving a session with 2d labels was fixed last week.
There were some errors or warnings trying to move 2d labels with the mouse -- I fixed that today.
You would have to be more specific than "I had problems with the visibility of 2D labels." Give a specific case which does not work as expected.

in reply to:  3 ; comment:3 by papai@…, 6 years ago 

Dear Tom,

Sorry for the vague description. I had a problem to move the 2D labels with the mouse. The labels didn’t move with the pointer. When I moved the mouse downward the label moved downward too, but not with the same speed. When I moved the mouse left or right, the label moved to the opposite direction.
There were also places where the label disappeared, so I couldn’t place them where I wanted.

Best regards,
Gabor
---
Gabor Papai
IGBMC
Integrated Structural Biology
1, rue Laurent Fries, Bp 10142
67404 Illkirch, France
Tel: +33-3-69485288

On 19 Aug 2019, at 21:03 , ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#2325: 2D labels: session save: LabelModel class not found; also some visibility
problems
-------------------------------+-------------------------
         Reporter:  papai@…   |      Owner:  Tom Goddard
             Type:  defect    |     Status:  closed
         Priority:  normal    |  Milestone:
        Component:  Graphics  |    Version:
       Resolution:  fixed     |   Keywords:
       Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
          Project:  ChimeraX  |
-------------------------------+-------------------------
Changes (by Tom Goddard):

* status:  assigned => closed
* resolution:   => fixed


Comment:

The error saving a session with 2d labels was fixed last week.
There were some errors or warnings trying to move 2d labels with the mouse
-- I fixed that today.
You would have to be more specific than "I had problems with the
visibility of 2D labels." Give a specific case which does not work as
expected.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2325#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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