[Chimera-users] command line > vol all surface level 0.1 colour gradient

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 20 08:00:43 PST 2021

Hi Dieter,
You need a separate "scolor" command for the coloring, in which you have to specify the model numbers of the surface to color and the volume that the gradient comes from (there is no "all" specification).  You would need a separate scolor command for each different volume being used to calculate the gradient.  For example

vol all style surface level 0.1
scolor #0 gradient #0 cmap rainbow
scolor #2 gradient #2 cmap rainbow

Syntax and options are explained in the "scolor" documentation:


You could find this with menu: Help... Search Documentation, e.g. searching for "volume gradient".

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 20, 2021, at 12:50 AM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Dear Elaine,
>      please forgive me for asking again, I cannot find your previous mail and my notes:
> How can I, in command line, do the following, i.e. what is the correct syntax?
> vol all style surface level 0.1 colour by gradient colours 5 palette rainbow set
> I have a number of volumes loaded and want to colour their surfaces, at level 0.1 by 'volume data gradient norm' with 5 rainbow colours setting them to the full range
> Thanks a lot, best Dieter

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