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Opened 6 years ago
Closed 6 years ago
#2577 closed defect (fixed)
Model whose ID is None being sorted by ID during model removal
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-11-14) Description Error after close command when using volume eraser. Log: UCSF ChimeraX version: 0.91 (2019-11-14) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1a0m format mmCIF fromDatabase pdb 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m #1 --- Chain | Description A B | α-conotoxin [TYR15]-epi Non-standard residues in 1a0m #1 --- NH2 — amino group > vr true started SteamVR rendering VR mode select > select /A:14 8 atoms, 7 bonds, 1 model selected > select /A:14 8 atoms, 7 bonds, 1 model selected > select up 42 atoms, 43 bonds, 1 model selected > select up 138 atoms, 118 bonds, 1 model selected > select down 42 atoms, 43 bonds, 1 model selected > select /A:11 8 atoms, 7 bonds, 1 model selected > select up 42 atoms, 42 bonds, 1 model selected > select up 138 atoms, 118 bonds, 1 model selected > select down 42 atoms, 42 bonds, 1 model selected > select up 138 atoms, 118 bonds, 1 model selected > select down 42 atoms, 42 bonds, 1 model selected > select /A:10 8 atoms, 7 bonds, 1 model selected > select down 8 atoms, 7 bonds, 1 model selected > select up 42 atoms, 42 bonds, 1 model selected > select up 138 atoms, 118 bonds, 1 model selected > select up 276 atoms, 242 bonds, 1 model selected > select up 276 atoms, 242 bonds, 2 models selected > select up 276 atoms, 242 bonds, 2 models selected > select up 276 atoms, 242 bonds, 2 models selected > select down 276 atoms, 242 bonds, 1 model selected > select down 138 atoms, 118 bonds, 1 model selected > select down 42 atoms, 42 bonds, 1 model selected > select up 138 atoms, 118 bonds, 1 model selected > select down 42 atoms, 42 bonds, 1 model selected > select up 138 atoms, 118 bonds, 1 model selected > select up 276 atoms, 242 bonds, 1 model selected > select down 138 atoms, 118 bonds, 1 model selected > select down 42 atoms, 42 bonds, 1 model selected > select down 8 atoms, 7 bonds, 1 model selected > select down 8 atoms, 7 bonds, 1 model selected VR mode move scene VR mode move scene VR mode zoom > open /Users/goddard/ucsf/presentations/milk-oct2019/casein-beta.pdb Chain information for casein-beta.pdb #2 --- Chain | Description A | No description available VR mode translate selected models VR mode rotate selected models VR mode translate selected models VR mode move scene No VR support for mouse mode pivot VR mode select > select clear > show atoms VR mode distance > distance #1/A:51@O #1/A:25@O Distance between 1a0m #1/A HOH 51 O and HOH 25 O: 5.835Å > ~distance #1/A:51@O #1/A:25@O > distance #2/A:208@HE2 #2/A:208@HH Distance between casein-beta.pdb #2/A TYR 208 HE2 and HH: 2.220Å > ~distance #2/A:208@HE2 #2/A:208@HH > distance #2/A:156@HE22 #2/A:208@HE2 Distance between casein-beta.pdb #2/A GLN 156 HE22 and TYR 208 HE2: 6.427Å > distance #2/A:156@HG3 #1/A:51@O Distance between casein-beta.pdb #2/A GLN 156 HG3 and 1a0m #1/A HOH 51 O: 5.951Å > ~distance #2/A:156@HG3 #1/A:51@O > ~distance #2/A:156@HE22 #2/A:208@HE2 VR mode label > label #2/A:156 color yellow bgColor dimgray size 64 height 0.7 > label delete residues > label #2/A:156 color yellow bgColor dimgray size 64 height 0.7 No VR support for mouse mode move label > label delete residues VR mode clip VR mode clip rotate VR mode zone > zone #2/A:156 ribbon false > zone #2/A:156 ribbon false > zone #2/A:156 ribbon false residueDistance 6.61 labelDistance 5.29 surfaceDistance 10.6 > zone #2/A:156 ribbon false residueDistance 8.62 labelDistance 6.9 surfaceDistance 13.8 > zone #2/A:156 ribbon false residueDistance 11.2 labelDistance 9 surfaceDistance 18 > zone #2/A:156 ribbon false residueDistance 8.49 labelDistance 6.8 surfaceDistance 13.6 > zone #2/A:156 ribbon false residueDistance 6.38 labelDistance 5.1 surfaceDistance 10.2 > zone #2/A:156 ribbon false residueDistance 4.87 labelDistance 3.89 surfaceDistance 7.79 > zone label false > zone clear > open 1547 fromDatabase emdb Opened emd_1547.map, grid size 160,160,160, pixel 2.8, shown at level 0.231, step 1, values float32 > close #1 > close #2 VR mode contour level > volume #3 level 0.9561 > volume #3 level 1.077 VR mode crop volume > volume #3 region 0,0,0,159,159,159 > volume #3 region 0,0,0,159,70,159 > volume #3 region 0,63,0,159,70,159 VR mode move planes > volume #3 region 0,81,0,159,88,159 VR mode clip > clip off VR mode tape measure > marker delete #1 VR mode pick blobs > measure blob #!3.1 triangleNumber 5894 color #0000ccff outline true Surface 1547 #3.1 blob: volume = 2761.1 area = 1796.3 size = 32.395 24.981 18.902 > measure blob #!3.1 triangleNumber 7462 color #7ec06fff outline true Surface 1547 #3.1 blob: volume = 3329.1 area = 2042.9 size = 37.37 30.576 19.008 > measure blob #!3.1 triangleNumber 6631 color #da5961ff outline true Surface 1547 #3.1 blob: volume = 544.4 area = 446.35 size = 19.244 8.7142 8.6296 > volume #3 level 1.208 VR mode map eraser > volume erase #3 center 47.919,21.964,-84.098 radius 51.083 > volume erase #2 center 20.382,-0.4032,86.204 radius 51.072 > close Traceback (most recent call last): File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 1833, in <lambda> dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e) File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 574, in close_request tool_instance.delete() File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map_eraser/eraser.py", line 230, in delete ses.models.close([self._sphere_model]) File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 629, in close mremoved = self.remove(models) File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 604, in remove mlist.sort(key=lambda m: len(m.id), reverse=True) File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 604, in <lambda> mlist.sort(key=lambda m: len(m.id), reverse=True) TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 604, in mlist.sort(key=lambda m: len(m.id), reverse=True) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.2.24 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Model whose ID is None being sorted by ID during model removal |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Closing map eraser tool window after the eraser sphere model was closed tried to close the sphere model again.
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That routine is a mixture of Tom and Greg code, with the most recent edits being Tom's, so assigning to Tom and cc'ing Greg. Part of the code seems to assume that the IDs can't be None, and another part tests whether they're None.