Hi Jacob,
On Wed, 2011-05-25 11:58 EDT, Jacob Keller
<[log in to unmask]> wrote:
> Dear Crystallographers,
>
> does anyone know of a program to compare multiple structures and
> identify which solvent molecules (water, ions, etc.) are conserved
> between the structures? I guess it would be nice also if it could
> identify when, for example, a Cl- in structure A was re-occupied by an
> HOH in B, or even some atom in a ligand being replaced by a water.
PyMOL's selection routines can allow something like this. To find all
waters and ions in one structure that are within 0.5 Angstroms (for
example) of the waters and ions in another structure you can type:
select conserved_waters, structure1 &! polymer &! organic within 0.5
of structure 2 &! polymer &! organic
You can then either save that selection to a file or iterate through it to
look at the details:
iterate conserved_waters, print chain,resn,resi,name
To search for an ion (or ligand atom) that replaces a water you could do:
select structure1 & r. hoh within 0.5 of structure1 &! polymer &! r. hoh
If you wanted to do this sort of thing on a large set of structures, then
it could be scripted in a more user-friendly way.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<[log in to unmask]> http://pldserver1.biochem.queensu.ca/~rlc
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