[phenixbb] alternate side chains conjugated with water molecules
pafonine at lbl.gov
Fri May 29 05:25:30 PDT 2015
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
> 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
> The closest to this I could find is:
> 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
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