VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Sun Oct 06 2002 - 13:37:35 CDT

Hi,

This question has come up before on the vmd mailing lists; the simple
reason is that VMD is using the same categorization as RasMol, which at
the time of VMD's writing was the most widely used molecular visualization
program. There are many hydrophobicity scales one could choose from,
so consistency with a de facto standard was not an unreasonable strategy.
For VMD the definition of hydrophobic is precisely
"resname ALA LEU VAL ILE PRO PHE MET TRP".

Note that recent 1.8a versions of VMD now allows you to define your
own atom selection macros, so you can create your own definitions of
hydrophobicity and use them in your atom selections (though you can't
override existing definitions). Let us know if you need any help
using them.

Thanks,

Justin

On Sun, Oct 06, 2002 at 12:42:20AM +0200, Markus Laub wrote:
> Hi there,
>
> how is the term hydrophobicity defined in VMD. Are amino Acids added
> to the hydrophobic group if the hydrophobicity is greater than or equal
> a certain level of for example the Kyte-Doolittle scale?
>
>
> Greetings,
>
> Markus
>
>
> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys