[PyMOL] How to compute the interface surface between ligand and protein?

[Thomas E. <te...@gm...>]

Greetings,

I want to compute the interface surface between the ligand and the protein
in batch mode for hundreds of thousands of PDBs, like the attached one
(sample.pdb). I am interested in the interface surface of both of them.
First I create two new molecules, the protein, and the ligand, and I work
with them because the results I get when working with the original molecule
(which contains both protein and ligand) are different.

load sample.pdb
> create protein, polymer
> create ligand, resn LIG
> delete sample
>
> select prot_interface, protein within 3.5 of ligand;
> set dot_solvent, 0;
> get_area prot_interface;
> set dot_solvent, 1;
> get_area prot_interface;
>
> select lig_interface, ligand within 3.5 of protein;
> set dot_solvent, 0;
> get_area lig_interface;
> set dot_solvent, 1;
> get_area lig_interface;


protein interface molecular surface = 1216.239 Angstroms^2
protein interface SASA = 763.095 Angstroms^2
ligand interface molecular surface = 748.867 Angstroms^2
ligand interface SASA = 977.608 Angstroms^2

I still don't understand why the interface molecular surface of the ligand
is smaller than the interface SASA, while the opposite happens with the
protein. Could someone please explain this to me and verify that I am
computing the interface surfaces correctly?

I thank you in advance.
Thomas



-- 

======================================================================

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic

email: te...@gm..., Twitter: tevangelidis
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