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
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)

in reply to:  1 ; comment:1 by Elaine Meng, 6 years ago

Oops mistyped one command into the ticket.

I did not really use “seg colors #1 map #1”, I used “seg colors #3 map #1"

comment:2 by Elaine Meng, 6 years ago

Component: UnassignedVolume Data
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionerror showing image map colored by index-map segmentation

comment:3 by Tom Goddard, 6 years ago

Resolution: fixed
Status: assignedclosed

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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