Thanks Robert, this really did the trick!
All the best,
Jacob Keller
On Wed, May 25, 2011 at 12:38 PM, Robert Campbell
<[log in to unmask]> wrote:
> 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
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
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