VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Mon Feb 28 2005 - 07:42:52 CST

hi all,

i guess this must have been asked before, but i couldn't find any
solution to my problem. i want to get list of all residues defining a
surface of my protein. i know i can do "surface" or "protein and not
buried" selection, but this doesn't seem to work ok. from what i've seen
in the documentation, "buried" is defined as
        residues named ALA LEU VAL ILE PHE CYS MET TRP
so if any of the other residues is "buried" inside the protein, it
doesn't work correctly. does this mean, that some kind of assumption
"hydrophobic = buried" is made?

is there any way how to get the desired information? will i'll have to
somehow parse surf/msms outputs?

thank you for help. best regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
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