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

matheus froeyen matheus.froeyen at gmail.com
Tue Sep 20 00:32:18 PDT 2011


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

In the surface color popup I need to select color surface "MSMS surface"
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
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