Hi Elaine, thank you for your help. Unfortunately, I wasn't able to get it to work, the command transparency asks for a value (percent) and doesn't recognize the $2 range as this value. I was able to get it to work with this instead: color #1 blue transparency #1.1 90 cartoon transparency #1.2 85 cartoon transparency #1.3 80 cartoon transparency #1.4 70 cartoon transparency #1.5 70 cartoon transparency #1.6 65 cartoon transparency #1.7 60 cartoon transparency #1.8 55 cartoon transparency #1.9 50 cartoon transparency #1.10 45 cartoon transparency #1.11 40 cartoon transparency #1.12 35 cartoon transparency #1.13 30 cartoon transparency #1.14 25 cartoon transparency #1.15 20 cartoon transparency #1.16 15 cartoon transparency #1.17 10 cartoon transparency #1.18 5 cartoon graphics silhouettes true Brute force but it works... Best Vincent Le 20/01/2023 à 17:52, Elaine Meng a écrit :
Hi Vincent, My first thought was simply to define the palette with transparent colors. However, to my surprise, this does not work (transparency in the palette is ignored)...
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
For example, to rainbow chains from opaque cyan to 80% transparent blue, I tried:
open 4hhb rainbow chains palette rgba(0.0,1.0,1.0,1.0):rgba(0.0,0.0,1.0,0.2)
...but this ignores the "alpha" value (1-transparency).
The long way is instead to use a series of "transparency" commands, one for each structure. This will preserve their existing colors, just change their transparency, e.g.:
transparency #2 80 target ars
("ars" means atoms, ribbons, surface... if you don't include that, default is surface only) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>
HOWEVER, the "perframe" command provides a sneaky way to loop and put the multiple transparency settings in a single command, e.g.
open 1plx tile style sphere perframe 'transparency #1.$1 $2 target ars' range 1,80 range 0,80 frames 80
In this perframe command, the first range substitutes $1, so it goes from 1plx model #1.1 to #1.80, and the second range substitutes the transparency value from 0 to 80%. Fancy! But it takes some thought and usually some trial and error to fabricate the correct "perframe" command. See the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 20, 2023, at 2:53 AM, vincent Chaptal via ChimeraX-users<chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I'm rendering a series of models using this command line (which works very well):
rainbow #1 structures palette cyan:blue
I would like to do the same but in a series of transparent models, with a range from 0 to 80 (or similar).
Is there a command for this, I couldn't find it? Thanks a lot. Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/