[chimerax-users] color palette in transprency ?

[vincent Chaptal]

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 at 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/

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