Opened 7 years ago

Closed 6 years ago

#1658 closed defect (can't reproduce)

Structure sequence returns NULL structure pointer

Reported by: ze_li@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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  

> open "/Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-WT/20181231
WT_monomerglycan_fitmap.cxs"

opened ChimeraX session  

> close session

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

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.pdb chain A to BALgp120model.pdb, chain A with 0
mismatches  
Associated BAL120model_wtmap-coot-1.pdb chain A to BALgp120model.pdb, chain A
with 0 mismatches  
Associated 4zmjmono.pdb chain B to 4zmjmono.pdb, chain B with 0 mismatches  
Associated BALgp41model.pdb chain A to BALgp41model.pdb, chain A with 0
mismatches  
Associated 4zmjtrimer.pdb chain A to 4zmjmono.pdb, chain B with 0 mismatches  
Associated 4zmjtrimer.pdb chain B to 4zmjmono.pdb, chain B with 0 mismatches  
Associated 4zmjtrimer.pdb chain C to 4zmjmono.pdb, chain B with 0 mismatches  
Associated 4zmjmono_wtmap-coot-0.pdb chain B to 4zmjmono.pdb, chain B with 0
mismatches  
  
opened ChimeraX session  

> close #15

> close #11

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

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

Error in saving session for "StructureSeq":  
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 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1103, in take_snapshot  
'structure': self.structure,  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++
18QPushButtonPrivate  
  

Unable to save "StructureSeq". Session might not restore properly.  

> open /Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-
WT/BAL120model_wtmap-coot-1.pdb

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 #11  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in BAL120model_wtmap-coot-1.pdb #11  
---  
NAG — (NAG)  
  
Associated BAL120model_wtmap-coot-1.pdb chain A to BALgp120model.pdb, chain A
with 0 mismatches  

> close #13

> show #!10 models

> hide #!10 models

> hide #!11 models

> show #!11 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> close #11

> open /Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-
WT/BAL41model_wtmap-coot-1.pdb

Summary of feedback from opening
/Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-WT/BAL41model_wtmap-
coot-1.pdb  
---  
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 #11  
---  
Chain | Description  
A | No description available  
  
Associated BAL41model_wtmap-coot-1.pdb chain A to BALgp41model.pdb, chain A
with 0 mismatches  

> hide #!11 models

> show #!11 models

> select #11.1

1 pseudobond, 1 model selected  

> ~select #11.1

Nothing selected  

> show #!6 models

> hide #!6 models

> close #6

> select #11

983 atoms, 1000 bonds, 1 pseudobond, 1 model selected  

> ui mousemode rightMode rotate selected models

> ui mousemode rightMode translate selected models

> ui mousemode rightMode rotate selected models

> ui mousemode rightMode translate selected models

> ui mousemode rightMode rotate selected models

> ui mousemode rightMode translate selected models

> fitmap #11 inMap #2

Fit molecule BAL41model_wtmap-coot-1.pdb (#11) to map 20181230_WT_monomer.mrc
falloff (#2) using 983 atoms  
average map value = 0.5854, steps = 56  
shifted from previous position = 3.89  
rotated from previous position = 6.12 degrees  
atoms outside contour = 344, contour level = 0.48496  
  
Position of BAL41model_wtmap-coot-1.pdb (#11) relative to
20181230_WT_monomer.mrc falloff (#2) coordinates:  
Matrix rotation and translation  
0.99635890 -0.08043156 -0.02827894 15.09174057  
0.07909024 0.99581839 -0.04572155 -4.68891996  
0.03183814 0.04331848 0.99855387 -10.44085079  
Axis 0.46296345 -0.31257861 0.82943321  
Axis point 69.92166442 185.66309727 0.00000000  
Rotation angle (degrees) 5.51826897  
Shift along axis -0.20740807  
  

> color #14 rgb(11,34,255)

> color #11 rgb(242,145,52)

> fitmap #7 inMap #2

Fit molecule 4zmjmono.pdb (#7) to map 20181230_WT_monomer.mrc falloff (#2)
using 4856 atoms  
average map value = 0.6233, steps = 52  
shifted from previous position = 1.95  
rotated from previous position = 0.0711 degrees  
atoms outside contour = 1464, contour level = 0.48496  
  
Position of 4zmjmono.pdb (#7) relative to 20181230_WT_monomer.mrc falloff (#2)
coordinates:  
Matrix rotation and translation  
-0.46365642 0.88600400 -0.00442298 29.27666789  
0.88601426 0.46364370 -0.00362772 83.28337169  
-0.00116349 -0.00560085 -0.99998363 158.70803631  
Axis -0.51785375 -0.85546493 0.00269182  
Axis point -10.65785478 0.00000000 79.47655918  
Rotation angle (degrees) 179.89084554  
Shift along axis -85.97982245  
  

> surface dust #2 size 15

> hide #!14 models

> show #!14 models

> hide #!7 models

> show #!7 models

> color #7 rgb(125,125,125)

> show #!12 models

> hide #!12 models

> 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.  
  

> 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  
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  




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

Change History (3)

comment:1 by Eric Pettersen, 7 years ago

Component: UnassignedSequence
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionStructure sequence returns NULL structure pointer

comment:2 by Eric Pettersen, 7 years ago

Status: acceptedfeedback

Hi,

Can you provide the session file you were using (/Users/zeli/Documents/Project/HIV/HIV_Structure/Nov29/HIV-WT/20190128

WT_monomerglycan_fitmap.cxs)? I can't really reproduce the problem otherwise. Thanks!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 6 years ago

Resolution: can't reproduce
Status: feedbackclosed

No feedback from user

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