Re: [Apbs-users] a question about protein surface electrostatics

[Nathan B. <ba...@bi...>]

Hello --

Per my other e-mail, are you able to generate isocontours as described in
http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_visualize_the_electrostatic_potential_around_my_biomolecule%3F#Isocontour_visualization?
 This will help us determine if the problem originates with the
rendering
or with the loading of the electrostatic potential.

Thanks,

Nathan

On Thu, Nov 26, 2009 at 5:50 AM, laraine liang <lar...@gm...>wrote:

> Hello everyone,
>
> I tried to generate an image of protein surface electrostatics
> following the instruction from
>
> http://cardon.wustl.edu/MediaWiki/index.php/How_do_I_visualize_the_electrostatic_potential_around_my_biomolecule%3F
>
> which is:
> Visualizing surface potentials
> Another popular method of electrostatic potential visualization maps
> the electrostatic potential to the biomolecular surface. Before
> proceeding, you may want to delete the two isocontours you just
> created using the Delete Rep in the Graphical Representations window.
>
> Go to the Graphical Representations window (Graphics →
> Representations... from the VMD Main window) and create a new
> representation of the molecule with the Create Rep button.
> Go to the "Draw style" tab of the Graphical Representations window and
> change Drawing Method to "Surf" and Coloring Method to "Volume".
> Go to the "Trajectory tab" of the Graphical Representations window and
> change the "Color Scale Data Range:" to -10 to 10 (or whatever your
> favorite values are).
> Based on your version of VMD and your personal preferences, you might
> want to change the color scale for this image. Go to Graphics →
> Colors... in the VMD Main window and select the "Color Scale" tab from
> the new "Color Controls" window. The traditional coloring scheme for
> electrostatics is "RWB" (in the Method menu).
>
>
> But still, as you could find in the attachment, I could not see the
> color difference.
> Any suggestions would be heartedly welcome.
>
> Best,
>
> Chaoning
>
> --
> Enrich my life~
>
>
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-- 
Nathan Baker (ba...@bi...)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/