[Chimera-users] color surface by electrostatic potential from apbs dx file
matheus.froeyen at gmail.com
Wed Sep 21 00:51:00 PDT 2011
Thanks for the quick answers!
On Tue, Sep 20, 2011 at 6:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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
> > 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
> > mathy
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