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Opened 7 years ago
Closed 7 years ago
#1582 closed defect (can't reproduce)
Volume Viewer deleted twice(?)
| Reported by: | Owned by: | Conrad Huang | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.0.0-x86_64-i386-64bit ChimeraX Version: 0.7 (2018-08-07) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.7 (2018-08-07) OpenGL version: 4.1 ATI-2.0.36 OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine OpenGL vendor: ATI Technologies Inc. How to cite UCSF ChimeraX open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/9D7-magenta- HC.mrc" Opened 9D7-magenta-HC.mrc, grid size 600,600,600, pixel 1.12, shown at level -7.31e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/9D7-red- Lchain.mrc" Opened 9D7-red-Lchain.mrc, grid size 600,600,600, pixel 1.12, shown at level -1.6e-06, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/14B10-blue- Lchain.mrc" Opened 14B10-blue-Lchain.mrc, grid size 600,600,600, pixel 1.12, shown at level -1.82e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/14B10-cyan- Hchain.mrc" Opened 14B10-cyan-Hchain.mrc, grid size 600,600,600, pixel 1.12, shown at level -2.27e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/18A7.mrc" Opened 18A7.mrc, grid size 600,600,600, pixel 1.12, shown at level 4.75e-06, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP1.mrc" Opened VP1.mrc, grid size 600,600,600, pixel 1.12, shown at level -0.000134, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP2.mrc" Opened VP2.mrc, grid size 600,600,600, pixel 1.12, shown at level -9.84e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP3.mrc" Opened VP3.mrc, grid size 600,600,600, pixel 1.12, shown at level -0.000112, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP4.mrc" Opened VP4.mrc, grid size 600,600,600, pixel 1.12, shown at level -6.08e-05, step 4, values float32 close #4-8 #1 #2 #3 #9 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP1.mrc" Opened VP1.mrc, grid size 600,600,600, pixel 1.12, shown at level -0.000134, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP2.mrc" Opened VP2.mrc, grid size 600,600,600, pixel 1.12, shown at level -9.84e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP3.mrc" Opened VP3.mrc, grid size 600,600,600, pixel 1.12, shown at level -0.000112, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/VP4.mrc" Opened VP4.mrc, grid size 600,600,600, pixel 1.12, shown at level -6.08e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/9D7-magenta- HC.mrc" Opened 9D7-magenta-HC.mrc, grid size 600,600,600, pixel 1.12, shown at level -7.31e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/9D7-red- Lchain.mrc" Opened 9D7-red-Lchain.mrc, grid size 600,600,600, pixel 1.12, shown at level -1.6e-06, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/14B10-blue- Lchain.mrc" Opened 14B10-blue-Lchain.mrc, grid size 600,600,600, pixel 1.12, shown at level -1.82e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/14B10-cyan- Hchain.mrc" Opened 14B10-cyan-Hchain.mrc, grid size 600,600,600, pixel 1.12, shown at level -2.27e-05, step 4, values float32 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/18A7.mrc" Opened 18A7.mrc, grid size 600,600,600, pixel 1.12, shown at level 4.75e-06, step 4, values float32 volume #1 0.6 Expected a keyword volume #1 level 0.6 volume #1-9 level 0.6 set bgColor white lighting full transparency #1 50 transparency #1 0 transparency #1 0.3 transparency #1 20 transparency #1 0 color #1 #377eb8 color #2 #33a02c color #3 #fb9a99 color #4 #ffed6f color #5 magenta color #6 orange color #7 blue color #8 cyan color #9 coral lighting soft open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/1.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 1.pdb #10 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available show selAtoms ribbons hide selAtoms transparency 50 lighting full transparency 70 transparency #1 0 transparency #2 0 transparency #3 0 view orient transparency 0 lighting full lighting soft lighting full lighting soft view orient lighting shadows true intensity 0.5 lighting soft lighting full lighting soft select up 3078 atoms, 3157 bonds selected delete sel delete sel select up 1582 atoms, 1615 bonds selected select up 1671 atoms, 1709 bonds selected delete sel select up 1323 atoms, 1349 bonds selected select up 1737 atoms, 1779 bonds selected select up 8195 atoms, 8411 bonds selected select up 1159 atoms, 1181 bonds selected delete sel select up 535 atoms, 544 bonds selected delete sel delete sel molmap #10 20 transparency #11 99 show #5-8 #1 #2 #3 #4 #9 target m view orient transparency #11 50 transparency #11 70 transparency #11 0 transparency #11 50 transparency #11 80 transparency #11 70 set silhouettes true set silhouettes false set silhouettes true lighting flat lighting flat set silhouettes false lighting soft set silhouettes true set silhouettes false set silhouettes true open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/2.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 2.pdb #12 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/3.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 3.pdb #13 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/4.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 4.pdb #14 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/5.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 5.pdb #15 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available hide #5-10 #1 #2 #3 #4 #11 target m hide selAtoms show selAtoms ribbons delete #12-15/H delete #12-15/L delete #12-15/J delete #12-15/K select up 11538 atoms, 11824 bonds selected select up 13320 atoms, 13672 bonds selected delete sele Missing or invalid "atoms" argument: invalid atoms specifier delete sel molmap #12-15 20 molmap #12 20 molmap #13 20 molmap #14 20 molmap #15 20 transparency #11,16-19 50 hide #12-14 #15 target m show #5-8 #1 #2 #3 #4 #9 target m transparency #11,16-19 80 transparency #1-4 50 transparency #1-4 30 transparency #11,16-19 99 transparency #1-4 0 transparency #11,16-19 20 transparency #11,16-19 30 transparency #11,16-19 40 lighting full lighting soft set silhouettes false set silhouettes true set silhouettes false set silhouettes true set silhouettes false set silhouettes true hide #16-18 #19 target m view orient transparency #11 50 view orient hide #5-9 #1 #2 #3 #4 #10 target m show #5-9 #1 #2 #3 #4 #10 target m show #16-18 #19 target m close #16-18 #19 close #11 molmap #10-15 20 transparency #11 50 transparency #11 50 view orient set silhouettes false set silhouettes true set silhouettes false set silhouettes true set silhouettes false toolshed show "Side View" view orient transparency #11 99 transparency #11 90 set silhouettes true open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/6.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 6.pdb #16 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/7.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 7.pdb #17 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/8.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 8.pdb #18 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/9.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 9.pdb #19 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/13.CA16-M-ThreeFabs/figure2-a/10.pdb" Opened PDB data containing 13196 atoms and 13538 bonds Chain information for 10.pdb #20 --- Chain | Description C | No description available D | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available U | No description available V | No description available W | No description available X | No description available hide #5-10 #1 #2 #3 #4 #11 target m hide selAtoms show selAtoms ribbons delete #16-20/H,L delete #16-20/K,j delete #16-20/V,X,U delete #16-20/w molmap #16-20 20 show #5-8 #1 #2 #3 #4 #9 target m hide #16-19 #20 target m transparency #21 90 view orient set silhouettes false set silhouettes true set silhouettes false view orient save /Users/maozhouhe/Desktop/CA16-mature-3Fabs.tiff width 2794 height 2576 supersample 4 transparentBackground false set silhouettes true lighting full lighting soft lighting full lighting soft set silhouettes false set silhouettes true set silhouettes false save /Users/maozhouhe/Desktop/CA16-mature-3Fabs-true.tiff width 2794 height 2576 supersample 4 transparentBackground true save /Users/maozhouhe/Desktop/CA16-mature-3Fabs--pent-true.tiff width 2794 height 2576 supersample 4 transparentBackground true set silhouettes true save /Users/maozhouhe/Desktop/CA16-mature-3Fabs--pent-true.tiff width 2794 height 2576 supersample 4 transparentBackground true save session "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/5.Merge/figure2/figure2-center.cxs" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. close session open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/3.Figure-manuscript/Figure3/5-fold- surfColor.cxs" format session opened ChimeraX session show #4 target m color zone #1 near #4 distance 5 color zone #1 near #4 distance 6 color zone #1 near #4 distance 8 color zone #1 near #4 distance 9 color zone #1 near #4 distance 12 color zone #1 near #4 distance 113 color zone #1 near #4 distance 13 color zone #1 near #4 distance 12 color zone #1 near #4 distance 12.5 color zone #1 near #4 distance 13 color #3/V,U gray color #4/V,U gray color #4/X,W purple color zone #1 near #4 distance 13 color #4/X,W #9370db color zone #1 near #4 distance 13 color #4/X,W #fa8072 color zone #1 near #4 distance 13 color #4/X,W red color zone #1 near #4 distance 13 color #4/X,W #9370db color zone #1 near #4 distance 13 color #4/X,W purple color zone #1 near #4 distance 13 color #4/X,W #9370db color zone #1 near #4 distance 13 color #4/V,U slateblue color zone #1 near #4 distance 13 color #4/V,U gray color zone #1 near #4 distance 13 toolshed show "Side View" lighting soft set silhouettes false set silhouettes true lighting full lighting soft lighting shadows true intensity 0.5 lighting soft lighting simple lighting simple lighting shadows true lighting soft set silhouettes false set silhouettes true set silhouettes false set silhouettes true set silhouettes false save /Users/maozhouhe/Desktop/CA16-M-18A7-5fold-Nov21.tiff width 2794 height 2576 supersample 4 transparentBackground true save session "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/3.Figure-manuscript/Figure3/5-fold- surfColor.cxs" Session file format is not finalized, and thus might not be restorable in other versions of ChimeraX. open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/8.5fold/CA16-Mature-18A7-Nov1th- Final.pdb" Opened PDB data containing 10966 atoms and 11284 bonds Chain information for CA16-Mature-18A7-Nov1th-Final.pdb #5 --- Chain | Description A B C D E | No description available H | No description available L | No description available hide selAtoms show selAtoms ribbons color #5/A,B,C,D,E #377eb8 color #5/L #9370db color #5/H gray style selAtoms ball Changed 6 atom styles style selAtoms stick Changed 6 atom styles show selAtoms surfaces hide selAtoms surfaces style selAtoms stick Changed 6 atom styles show selAtoms style selAtoms sphere Changed 6 atom styles style selAtoms sphere Changed 6 atom styles style selAtoms ball Changed 6 atom styles style selAtoms stick Changed 6 atom styles color selAtoms byhetero hide selAtoms ribbons style selAtoms stick Changed 6 atom styles show selAtoms ribbons show selAtoms ribbons hide selAtoms ribbons style selAtoms ball Changed 6 atom styles hide selAtoms surfaces style selAtoms ball Changed 6 atom styles style selAtoms stick Changed 6 atom styles hide selAtoms show selAtoms show selAtoms ribbons hide selAtoms ribbons show #5/L@n,ca,c,o style stick #5/L@n,ca,c,o Expected a keyword style #5/L@n,ca,c,o stick Changed 452 atom styles style #5/L@n,ca,c,o stick ringFill on Expected a keyword style #5/L@n,ca,c,o stick ringFill thick Expected a keyword style #5/L@n,ca,c,o stick Changed 452 atom styles show selAtoms surfaces hide #5.4,5-7 target m hide selAtoms surfaces close #5.1-3,5-7,4 close #4.2-9,15,17-18,20-25,10,11,12,13,14,16,19 close #3.2-7,9-10,17-21,8,11,12,13,14,15,16 close #2.1,2-7 close #5 open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/8.5fold/Final- model/CA16-Mature-18A7-Nov1th-Final_real_space_refined-coot.pdb" Summary of feedback from opening /Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/2.Model/8.5fold/Final- model/CA16-Mature-18A7-Nov1th-Final_real_space_refined-coot.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.006 0.164 11286 Ignored bad PDB record found on line 23 ANGLE : 0.952 23.404 15341 Ignored bad PDB record found on line 24 CHIRALITY : 0.055 0.248 1630 16 messages similar to the above omitted Opened PDB data containing 10869 atoms and 11189 bonds Chain information for CA16-Mature-18A7-Nov1th-Final_real_space_refined- coot.pdb #5 --- Chain | Description A B | No description available C D E | No description available H | No description available L | No description available hide selAtoms show selAtoms ribbons color #5/A,B,C,D,E #377eb8 color #5/L #9370db color #5/H gray hide selAtoms ribbons show selAtoms ribbons hide selAtoms lighting soft lighting shadows true intensity 0.5 lighting simple lighting full close session open "/Users/maozhouhe/Document/NIDVD/1. Manuscript_preparation/CVA16_netrulization/5.Merge/figure2/figure2-center.cxs" format session opened ChimeraX session Traceback (most recent call last): File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py", line 1147, in <lambda> dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py", line 485, in close_request tool_instance.delete() File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/map/volume_viewer.py", line 124, in delete super().delete() File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/tools.py", line 176, in delete self.session.tools.remove([self]) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/tools.py", line 368, in remove del self._tool_instances[tid] KeyError: 10 KeyError: 10 File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/tools.py", line 368, in remove del self._tool_instances[tid] See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. OpenGL version: 4.1 ATI-2.0.36 OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 7 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Volume Viewer deleted twice(?) |
comment:2 by , 7 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Tried several things but could not reproduce. We can catch the error and mask it, but I really want to fix the underlying problem. Maybe we can get more information next time.
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Somehow a Volume Viewer window survived through a session close/restore when the tool didn't? I tried various things and couldn't reproduce it.
--Eric