VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 16 2008 - 01:59:34 CDT

Hi,
  The default VMD atom selection macro "hydrophobic" is defined as follows:
hydrophobic resname ALA LEU VAL ILE PRO PHE MET TRP

You can redefine this macro to suit your needs as necessary...
As you can see, it's just a simple atom selection macro and nothing
more sophisticated. You can see the definitions of this and other
atom selection macros in the graphics form under the selection tab.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 02, 2008 at 04:16:29PM -0700, Giovanni Bellesia wrote:
> Hi,
> I have a quick one about the keyword "hydrophobic" used by the Graphics
> form.
> What hydrophobicity scale is used by vmd to define "hydrophobic" residues ?
>
> Thanks
> Giovanni 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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