[phenixbb] Van der waals interaction in phenix

[Nathaniel Echols]

On Mon, Jul 16, 2012 at 1:08 AM, subhash bihani <subhashbihani at gmail.com>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
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