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#2736 closed defect (fixed)
all-same-value attribute coloring yields black instead of 'mid' color
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.91 (2019-12-23) Description `color byattr` yields a jet-black model when all the attribute values are equal. Effectively invisible on the default background. Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3io0 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > color byattribute occupancy #1 1658 atoms, 230 residues, atom occupancy range 1 to 1 OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (7)
comment:1 by , 6 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → all-same-value attribute coloring yields black instead of 'mid' color |
comment:2 by , 5 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
| Status: | accepted → assigned |
comment:3 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Color byattribute uses a red/white/blue colormap with all 3 values assigned data value 1 since no range is specified and all occupancy values are 1. You would probably want to specify "range 0,1" in this case. But if you don't I agree you should get red, white, or blue and not black. So now it gives blue. I don't think any one of the colors is more correct in this degenerate situation. Color by attribute could easily see the range has just one value and do something different, but I'm not sure what.
comment:4 by , 5 years ago
Did the changes get pushed? I'm not seeing any changes in std_commands/color.py or surface/colorvol.py and after re-installing std_commands and surface I still get black coloring.
follow-up: 5 comment:5 by , 5 years ago
Change is in the map bundle where the colormap interpolation C++ code lives.
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The problem is that std_commands.color._value_colors returns all black (which isn't even in the palette) when the values are all the same. Under the hood it calls into colormap-processing routines in chimerax.surface. I believe those routines would need to be enhanced to handle this situation.