Opened 6 years ago
Closed 6 years ago
#2886 closed defect (fixed)
error showing image map colored by index-map segmentation
Reported by: | Elaine Meng | Owned by: | Tom Goddard |
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Priority: | normal | Milestone: | |
Component: | Volume Data | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-02-26) Description error showing image map colored by index-map segmentation setup: open 0557 from emdb vol threshold #1 min 0 vol scale #2 value uint8 ... after which I did several other things so unclear if this will be easily reproducible... but the error occurred after vol #1 style image seg colors #1 map #1 [... at that point vol #1 was hidden so I used Model Panel checkbox] show #!1 models ...Traceback Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start toolshed show $1 > alias whereprefs info path user unversioned config > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available > alias btut open > http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding- > sites.html > alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2 > value uint8; open 6nzk executed startup.cxc UCSF ChimeraX version: 0.92 (2020-02-26) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > segtest Summary of feedback from opening 0557 fetched from emdb --- note | Fetching compressed map 0557 from ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-0557/map/emd_0557.map.gz Opened emd_0557.map, grid size 400,400,400, pixel 1.05, shown at level 0.0747, step 2, values float32 Summary of feedback from opening 6nzk fetched from pdb --- notes | Fetching compressed mmCIF 6nzk from http://files.rcsb.org/download/6nzk.cif Fetching CCD MJJ from http://ligand-expo.rcsb.org/reports/M/MJJ/MJJ.cif 6nzk title: Structural basis for human coronavirus attachment to sialic acid receptors [more info...] Chain information for 6nzk #4 --- Chain | Description A B C | Spike surface glycoprotein Non-standard residues in 6nzk #4 --- BMA — β-D-mannose MAN — α-D-mannose MJJ — methyl 9-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto- non-2-ulopyranosidonic acid NAG — N-acetyl-D-glucosamine > segmentation surfaces #3 where 4 color blue Created 1 segmentation surfaces, 24360 triangles, subsampled 1 > hide #!3 models > close #5 > molmap strand 8 > segmentation colors #3 map #5 segmentation colors: Volume size 66,69,69 does not match segmentation size 400,400,400 > segmentation colors #3 surface #5 Colored surface surface (#5.1) with 6 segments > volume #5 level 0.2124 > segmentation colors #3 surface #5 Colored surface surface (#5.1) with 5 segments > hide #!4 models > volume #5 level 0.3674 > segmentation colors #3 surface #5 Colored surface surface (#5.1) with 6 segments > segmentation colors #3 surface #5 outsideColor pink Colored surface surface (#5.1) with 6 segments > volume #1 style image > segmentation colors #3 map #1 > hide #!5 models > show #!1 models Traceback (most recent call last): File "/Users/chimera/Applications/ChimeraX_Daily.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 "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 3661, in _update_drawings v.update_drawings() File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 696, in update_drawings self._update_image() # Create image File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 766, in _update_image self._image = im = VolumeImage(self) File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 1768, in __init__ s.mask_colors = v.mask_colors NameError: name 's' is not defined Error processing trigger "graphics update": NameError: name 's' is not defined File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py", line 1768, in __init__ s.mask_colors = v.mask_colors See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation
Change History (3)
comment:2 by , 6 years ago
Component: | Unassigned → Volume Data |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → error showing image map colored by index-map segmentation |
comment:3 by , 6 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
Fixed.
Segmentation coloring on a map which was never shown in image style then switching to image style caused this bug.
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