[phenixbb] Van der waals interaction in phenix

Pavel Afonine pafonine at lbl.gov
Mon Jul 16 08:21:50 PDT 2012


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!


On 7/16/12 7:57 AM, Nathaniel Echols wrote:
> On Mon, Jul 16, 2012 at 1:08 AM, subhash bihani 
> <subhashbihani at gmail.com <mailto: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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120716/b0f658b5/attachment.htm>

More information about the phenixbb mailing list