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

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 20 09:24:00 PDT 2011

Hi Mathy,
Maybe it is confusing because the surfcolor command is not connected to the settings in the Surface Color dialog.  The electrostatic potential file is actually one type of volume data, so I'm not sure what you mean when you say the surface is colored by volume data, not by electrostatic potential. 

For Surface Color, the only difference in treatment of electrostatic potential and other volume data is the default dialog settings, and these are not connected to the command. 

If using the scolor command to color by electrostatic potential, you will probably want to use the "offset 1.4" option, 

which corresponds to the "surface offset" option in the Surface Color dialog when it is set to show electrostatic potential.  There should not be any need to use the dialog when you are using the command.

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

On Sep 20, 2011, at 12:32 AM, matheus froeyen wrote:

> 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

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