[phenixbb] alternate side chains conjugated with water molecules

Pavel Afonine pafonine at lbl.gov
Fri May 29 05:25:30 PDT 2015

Hi Jorge,

I'm sorry for delay with replying. I was (and am) traveling May 18-29, 
so it happens I miss emails by accident or do not reply promptly. Sorry.

What you describe is definitely possible to do in Phenix, I have helped 
others to do similar things in the past and all worked just fine.

I think it is easiest if you send me model and data files and tell what 
particular residues need to be couples with water, and then I will send 
you back a working example.

Once again, I am sorry for the delay and I'm looking forward to help you 
with this problem.


On 5/16/15 9:29 PM, Jorge Iulek wrote:
> Dear all,
>     I have a 1.70 A resolution dataset in which I observe, with 
> certain confidence, that some (few) side chains are alternated with 
> waters.
>     Though managing to tie occupancies of each alternate side chain 
> with a water molecule to give an overall occupancy of 1.00, phenix 
> refine still pushes them (water from side chain) apart as if there 
> were bumping restraints (but their occupancies sum up to no more than 
> 1.00).
>     The closest to this I could find is:
> http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html
>     But I could not find how to turn off specific bumping restraints.
>     I would be thankful if someone could point me to the recipe to do 
> this.
> Jorge

More information about the phenixbb mailing list