Opened 6 years ago

Last modified 6 years ago

#2789 assigned defect

Attempted instantiation of HeaderSequence during session save

Reported by: pett@… Owned by: Greg Couch
Priority: major Milestone:
Component: Sessions Version:
Keywords: Cc: noemi.ruiz@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.92 (2020-01-29)
Description
(Describe the actions that caused this problem to occur here)
save sessiion after VR

Log:
UCSF ChimeraX version: 0.92 (2020-01-29)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:\cp2.cxs

Summary of feedback from opening E:\cp2.cxs  
---  
warning | registering illegal selector name "6F5"  
  
opened ChimeraX session  

> select #3/M:37

9 atoms, 8 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

> vr true

started SteamVR rendering  

> view

VR mode translate selected models  
VR mode translate selected models  
VR mode translate selected models  
VR mode translate selected models  
VR mode select  

> select #3

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  
VR mode translate selected models  
VR mode translate selected models  

> open 1hzh

Summary of feedback from opening 1hzh fetched from pdb  
---  
notes | Fetching compressed mmCIF 1hzh from
http://files.rcsb.org/download/1hzh.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif  
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif  
Fetching CCD GAL from http://ligand-expo.rcsb.org/reports/G/GAL/GAL.cif  
Fetching CCD FUC from http://ligand-expo.rcsb.org/reports/F/FUC/FUC.cif  
  
1hzh title:  
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]  
  
Chain information for 1hzh #5  
---  
Chain | Description  
H K | immunoglobulin heavy chain  
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein  
  
Non-standard residues in 1hzh #5  
---  
BMA — β-D-mannose  
FUC — α-L-fucose  
GAL — β-D-galactose  
MAN — α-D-mannose  
NAG — N-acetyl-D-glucosamine  
  
  

> select #5

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  
VR mode select  

> select up

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  

> select up

39694 atoms, 39540 bonds, 2 pseudobonds, 7 models selected  

> select up

39694 atoms, 39540 bonds, 5 pseudobonds, 10 models selected  
VR mode move scene  

> select clear

> open 1hzh

1hzh title:  
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]  
  
Chain information for 1hzh #6  
---  
Chain | Description  
H K | immunoglobulin heavy chain  
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein  
  
Non-standard residues in 1hzh #6  
---  
BMA — β-D-mannose  
FUC — α-L-fucose  
GAL — β-D-galactose  
MAN — α-D-mannose  
NAG — N-acetyl-D-glucosamine  
  
  
VR mode select  

> select clear

> select clear

> select clear

> select #6

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  

> open 1hzh

1hzh title:  
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]  
  
Chain information for 1hzh #7  
---  
Chain | Description  
H K | immunoglobulin heavy chain  
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein  
  
Non-standard residues in 1hzh #7  
---  
BMA — β-D-mannose  
FUC — α-L-fucose  
GAL — β-D-galactose  
MAN — α-D-mannose  
NAG — N-acetyl-D-glucosamine  
  
  

> select #7

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  
VR mode tape measure  

> marker delete #8

> toolshed show "Basic Actions"

> select ep6F11

14 atoms, 12 bonds, 1 model selected  

> select ep6F13

16 atoms, 14 bonds, 1 model selected  

> select ep6F15

13 atoms, 11 bonds, 1 model selected  

> select ep6F5

9 atoms, 8 bonds, 1 model selected  

> help label

VR mode select  

> vr false

> select ep6F5

9 atoms, 8 bonds, 1 model selected  

> view sel

> label ep6F5 text 6F5

> select ep6F11

14 atoms, 12 bonds, 1 model selected  

> view sel

> label #4:461 text 6F11

> label #4:651 text 6F11

> select ep6F13

16 atoms, 14 bonds, 1 model selected  

> view sel

> label ep6F13 text 6F13

> select ep6F15

13 atoms, 11 bonds, 1 model selected  

> view sel

> label #4:1017,1039 text 6F15

> view

> vr true

started SteamVR rendering  

> select clear

> select #7

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  

> marker delete #8

VR mode move scene  
VR mode translate selected models  
VR mode select  
VR mode select  

> select clear

> select clear

> select clear

> select clear

VR mode select  
VR mode select  

> select clear

> select #6

10647 atoms, 10877 bonds, 2 pseudobonds, 2 models selected  
VR mode translate selected models  
VR mode select  
VR mode select  
VR mode select  
VR mode select  

> vr false

> ~select

Nothing selected  

> save session E:/positioned.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 288, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 210, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 205, in _copy  
return data.__class__(items)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 205, in _copy  
return data.__class__(items)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\ui\gui.py", line 925, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\ui\gui.py", line 643, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 1100, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 992, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\commands\save.py", line 64, in save  
_handle_unexpected_keyword_error(e, 5)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\session.py", line 288, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 210, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 204, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 205, in _copy  
return data.__class__(items)  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
TypeError: __init__() missing 1 required positional argument:
'refresh_callback'  
  
File "C:\Program Files\ChimeraX-Jan-29-2020\bin\lib\site-
packages\chimerax\core\state.py", line 205, in _copy  
return data.__class__(items)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.39
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Priority: normal → major
Project: → ChimeraX
Reporter: changed from chimerax-bug-report@… to pett@…
Status: new → assigned
Summary: ChimeraX bug report submission → Attempted instantiation of HeaderSequence during session save

Not sure why this instantiation is occurring during the session "discovery" processing. HeaderSequence is in the alignment_hdrs bundle.

comment:2 by Eric Pettersen, 6 years ago

I'm not sure why this would matter, but perhaps the fact that HeaderSequence inherits from list has something to do with it?

comment:3 by Eric Pettersen, 6 years ago

Cc: noemi.ruiz@… added
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