From: Giovanni Bellesia (
Date: Wed Jul 16 2008 - 02:13:46 CDT

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.


> 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
> 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.
Phone: 805 893 2767