Re: [chimerax-users] color palette in transprency ?

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 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