[Chimera-users] color surface by electrostatic potential from apbs dx file

[Tom Goddard]

Hi Mathy,

   You are right that the surface color dialog does not update when you 
use the scolor command.  I'll add that to our feature request list.  
Everything you are doing is right, just need to add the "offset 1.4" 
option to the scolor command so that the interpolated potential values 
are take 1.4 Angstroms from the surface.

scolor #0 volume #1 cmap -15,red:-5,yellow:0,green:5,cyan:15,blue offset 1.4

     Tom


> Hi
>
> I try to show the electrostatic potential calculated by apbs and 
> written to a pot.dx file.
> This works fine when using the mouse / menus.
>
> However I try to do this also using the command line interface
> because I need to repeat it many times.
>
> $ chimera chimera.cmd
>
> $ cat chimera.cmd:
>
> open prod30.pdb
>
> ~ribbon :
> ~fillring :
> surface :
>
> open pot.dx
> ~scolor #0
> scolor #0 volume #1 cmap rainbow
> scolor #0 volume #1 cmap -15,red:-5,yellow:0,green:5,cyan:15,blue
>
>
> I don't get an error but the surface is colored by volume data, not by 
> electrostatic potential.
> Also the popup window "Surface Color" is not updated for the selected 
> colors.
>
> In the surface color popup I need to select color surface "MSMS 
> surface" again,
> change "volume data value" to "electrostatic potential"
> and then push the button "Color". Then I get what I want, but 
> unfortunately using the mouse again.
>
> This should be done by the script too, I guess?
>
> I m using the last stable chimera 64 version for unix on redhat.
>
> best regards
> mathy