Re: [phenixbb] Van der waals interaction in phenix

Hi, two things: - make sure the altlocs of the residue and water are non-blanc and *different*. For example: set residue altloc to A and water altloc to B (if you make then the same they will be pushed apart by non-bonded repulsion term!); AND - make sure their occupancies are constrained during refinement such that: occupancy(residue) + occupancy(water)=1. This can be done either manually by defining constrained groups as described in the documentation page below (preferred option) or make sure the water and residue have the same chain id and residue number. Let me know if you have any questions or need any help with this! Pavel On 7/16/12 7:57 AM, Nathaniel Echols wrote:

On Mon, Jul 16, 2012 at 1:08 AM, subhash bihani mailto:[email protected]> wrote:

In one of my structure I have to put some water molecule in alternate confimation with amino acid residues and in another case with ligand. How do I do it in Phenix.

You just need to make sure the "altloc" identifier in the PDB file is set correctly for the atoms of interest. Currently this requires opening the file in a text editor, but I hope to have a better solution available very soon. The water molecule should have the same altloc as the amino acid residues which you want it to interact with - that is, if you set the altloc for the residues to A, the water also needs to be A. You may want to constrain the occupancies to be the same; see the manual here:

https://www.phenix-online.org/documentation/refinement.htm#anch111

-Nat