Unexpected None data given to StructureSeq.restore_snapshot()

[ze_li@…]

The following bug report has been submitted:
Platform:        Darwin-17.3.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-26)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-01-26)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Summary of feedback from opening files  
---  
warning | Start residue of secondary structure not found: HELIX 2 2 LEU A 45
ALA A 47 1 3  
  
  
  
BAL41model_wtmap-coot-1.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for BAL41model_wtmap-coot-1.pdb #1.1  
---  
Chain | Description  
A | No description available  
  
BAL120model_wtmap-coot-1.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for BAL120model_wtmap-coot-1.pdb #1.2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in BAL120model_wtmap-coot-1.pdb #1.2  
---  
NAG — (NAG)  
  

> set bgColor white

> hide #!1 models

  
  
BAL41model_wtmap.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for BAL41model_wtmap.pdb #2.1  
---  
Chain | Description  
A | No description available  
  
BAL120model_wtmap.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for BAL120model_wtmap.pdb #2.2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in BAL120model_wtmap.pdb #2.2  
---  
NAG — (NAG)  
  

> show #!1 models

> hide #!1 models

> hide #2 atoms

> select #2.1/A:36-56

169 atoms, 169 bonds, 1 model selected  

Unknown command: namesel hr1n  

> help name

> name hr1n #2.1/A:36-56

> name loopV1 #2.2/A:135-155

> name list

hr1n #2.1/A:36-56  
loopV1 #2.2/A:135-155  

Expected an objects specifieror a keyword  

> select loopV1

150 atoms, 149 bonds, 1 model selected  

> color loopV1 rgb(45,152,31)

> color hr1n rgb(45,152,31)

> show #!1 models

> hide #!1 models

> color #2.1 rgb(242,145,52)

> color hr1n rgb(45,152,31)

> select up

171 atoms, 170 bonds, 1 model selected  

> color #2.2 rgb(11,34,255)

> color loopV1 rgb(45,152,31)

> open /Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-
WT/20181217_WT_Trimer.mrc

Opened 20181217_WT_Trimer.mrc, grid size 128,128,128, pixel 2.2, shown at
level 0.503, step 1, values float32  

> hide #!3 models

> open /Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-
WT/4zmjmono_wtmap.pdb

4zmjmono_wtmap.pdb title:  
Crystal structure of ligand-free BG505 sosip.664 hiv-1 env trimer [more
info...]  
  
Chain information for 4zmjmono_wtmap.pdb #4  
---  
Chain | Description  
B | envelope glycoprotein GP160  
G | envelope glycoprotein GP160  
  
Non-standard residues in 4zmjmono_wtmap.pdb #4  
---  
BMA — β-D-mannose  
MAN — α-D-mannose  
NAG — N-acetyl-D-glucosamine  
  

> show #!3 models

> hide #!3 models

> hide #4 atoms

> color #4 rgb(125,125,125)

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> color #2.2:309-409 rgb(234,51,35)

> color #4 rgb(125,125,125)

> color #2.2 rgb(11,34,255)

> color #2.2:399-409 rgb(234,51,35)

> color loopV1 rgb(45,152,31)

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> close #3

> show #!2 models

> color #2.2:184-195 rgb(234,51,35)

> color #2.2:184-187 rgb(234,51,35)

> color #2.2:184-187 rgb(11,34,255)

> color #2.2:399 rgb(11,34,255)

> pwd

Current working directory is: /Users/zeli/Desktop  

> cd ..

Current working directory is: /Users/zeli  

> cd Documents

Current working directory is: /Users/zeli/Documents  

> cd Project

Current working directory is: /Users/zeli/Documents/Project  

> cd HIV_Structure

[Errno 2] No such file or directory: 'HIV_Structure'  

> cd HIV-Structures

[Errno 2] No such file or directory: 'HIV-Structures'  

> cd HIV_Structures

[Errno 2] No such file or directory: 'HIV_Structures'  

> cd HIV/HIV_Structure/Nov29/HIV-WT

Current working directory is:
/Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-WT  

> save BALmodel_vs_4zmjmonomer.png pixelSize 0.15

> save session /Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-
WT/20190128_WT_overrall_map_withBALmodel.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> close session

> close session

> open "/Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-WT/20190128
WT_monomerglycan_fitmap.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 594, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1070, in restore_snapshot  
sseq = StructureSeq(chain_id=data['chain_id'], structure=data['structure'])  
TypeError: 'NoneType' object is not subscriptable  
  
Summary of feedback from opening
/Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-WT/20190128
WT_monomerglycan_fitmap.cxs  
---  
notes | Associated 4zmjmono.pdb chain G to 4zmjmono.pdb, chain G with 0
mismatches  
Associated BALgp120model.pdb chain A to BALgp120model.pdb, chain A with 0
mismatches  
Associated 4zmjmono_wtmap-coot-0.pdb chain G to 4zmjmono.pdb, chain G with 0
mismatches  
Associated BAL120model_wtmap-coot-1.pdb chain A to BALgp120model.pdb, chain A
with 0 mismatches  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3421, in _update_drawings  
if v.display:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "graphics update": object of type 'NoneType' has no
len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-1.60.24
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

It seems unreasonable to have every restore_snapshot() method have to guard against being passed None as an argument rather than the expected data dictionary.

[pett]

session originally attached to #1732

[Conrad Huang]

For 0.9, make failure to save raise bug report dialog instead of just a warning. No session file should be written.

For 1.0, after save failure, offer a best-effort save which should not generate error on restore.

[Greg Couch]

Made failure to save raise bug report dialog instead of just a warning.

[Greg Couch]

Revised code to not (over)write session file when there is an error. Changed low-level code to raise exception rather than report it, and have it reported where we can decide to delete the temporary file, rather then rename it.