Transparency retained when coloring

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-13)
Description
Hi,

Not sure if this is a bug but it seems unexpected to me. If I define a color that has some degree of transparency (e.g. color name part_invisible 0,0,0,10), and use that to color a model, when I subsequently apply a color that doesn't have tranparency (e.g. a built in color like cornflower blue), the model retains the transparency from the first color. This is not how it worked in Chimera, and is not how I would expect it to work - is this the intended behavior?

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> volume voxelLimit 100000 showPlane false limitVoxelCount false
voxelLimitForOpen 10000

> alias crosshairs_on log text crosshairs_on: displays crosshairs at center of
rotation and places cofr at center of view; cofr centerofview showpivot 5,0.2

> alias crosshairs_off cofr centerofview showpivot false

> alias cootmode volume style mesh step 1 squaremesh false meshlighting true
twosidedlighting false capfaces false; surface cap false; size stickradius
0.05; ~rib; color gold target a; color byhet; lighting flat; lighting
depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set subdivision 1;
crosshairs_on; color #3333851effff target s; style stick; set bgcolor black

> alias cootmode_white volume style mesh step 1 squaremesh false meshlighting
true twosidedlighting false capfaces false; surface cap false; size
stickradius 0.05; ~rib; color orange target a; color byhet; lighting flat;
lighting depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set
subdivision 1; crosshairs_on; color #00000000cccc target s; style stick; set
bgcolor white

> alias carve surface zone #* nearatoms sel distance $1 maxcomponents 1

> alias uncarve surface unzone #*

> alias focus view cofr false

> alias saturation_down color modify $1 saturation - 10

> alias saturation_up color modify $1 saturation + 10

> alias lightness_up color modify $1 lightness + 5

> alias lightness_down color modify $1 lightness - 5

> alias hue_up color modify $1 hue + 5

> alias hue_down color modify $1 hue - 5

UCSF ChimeraX version: 0.91 (2019-06-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb

Chain information for
last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #1  
---  
Chain | Description  
A B G I | No description available  
C D E K | No description available  
F H J O | No description available  
  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color name invisible 0,0,0,0

Color 'invisible' is 100% transparent, 0% red, 0% green, and 0% blue

  

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> help lighting

> lighting depthCueColor invisible

> select up

Nothing selected  

> color name part_invisible 0,0,0,50

Color 'part_invisible' is 50% transparent, 0% red, 0% green, and 0% blue

  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1 part_invisible

> color "cornflower blue"

> color name part_invisible 0,0,0,90

Color 'part_invisible' is 10% transparent, 0% red, 0% green, and 0% blue

  

> color #1 part_invisible

> color name part_invisible 0,0,0,10

Color 'part_invisible' is 90% transparent, 0% red, 0% green, and 0% blue

  

> color #1 part_invisible

> color "cornflower blue"




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

This is the intended behavior -- allowing you to change colors while preserving transparency. If you explicitly specify transparency by providing RGBA then it does set the transparency. You can say "color cornflowerblue transp 0" if you want to also change transparent to opaque. That color is independent of transparency is only unexpected behavior if you are used to Chimera.

[olibclarke@…]

Ah - got it - that makes sense, I guess I am too used to Chimera

Oli