VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 16 2008 - 02:47:41 CDT

Giovanni,
  Offhand I don't know the answer. I think macro was written by
one of the students in our group eons ago based on older/previous
hard-coded tables. If I recall correctly, I think the list of
residues may predate my involvement with VMD, so I don't have much
history on it for you. This is one of those things that'd
be nice to have a 1-line comment for in the script :-)

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 16, 2008 at 12:13:46AM -0700, Giovanni Bellesia wrote:
> Thanks John,
> I am aware of the definition of the "hydrophobic" macro.
> I was just wondering (1) what hydropathy scale was considered when the
> macro was built (Kyte and Doolittle one f.e. is quite popular but there
> are many others in the literature) and (2) how the scale was divided in
> two sets (hydrophobic and polar/charged AA).
> I'm just asking for the sake of curiosity since the definition of
> "hydrophobic" and "polar/charged" AA is not unique.
>
> Giovanni
>
>
>
> >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
> >>
> >
> >
>
>
> --
> ------------------------------------------
> Giovanni Bellesia
> Department of Chemistry and Biochemistry
> University of California, Santa Barbara
> Santa Barbara, California 93106-9510, USA.
> Email: gbellesia_at_chem.ucsb.edu
> Phone: 805 893 2767
> Web: http://www.chem.ucsb.edu/~sheagroup/
> ------------------------------------------ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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