Thanks Robert, this really did the trick! All the best,
Jacob Keller On Wed, May 25, 2011 at 12:38 PM, Robert Campbell <[email protected]> wrote: > Hi Jacob, > > On Wed, 2011-05-25 11:58 EDT, Jacob Keller > <[email protected]> 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 > <[email protected]> http://pldserver1.biochem.queensu.ca/~rlc > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************
