Opened 7 years ago
Closed 6 years ago
#1658 closed defect (can't reproduce)
Structure sequence returns NULL structure pointer
Reported by: | Owned by: | Eric Pettersen | |
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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 , 7 years ago
Component: | Unassigned → Sequence |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Structure sequence returns NULL structure pointer |
comment:2 by , 7 years ago
Status: | accepted → feedback |
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comment:3 by , 6 years ago
Resolution: | → can't reproduce |
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Status: | feedback → closed |
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Hi,
WT_monomerglycan_fitmap.cxs)? I can't really reproduce the problem otherwise. Thanks!
--Eric