[phenixbb] alternate side chains conjugated with water molecules
iulek at uepg.br
Sun May 31 04:59:13 PDT 2015
Thank you for responding.
I put this structure in stand by for a while, then I retook now.
I tried some alternate possibilities. It seems to be mandatory that
the in constrained group selection, sidechain altloc B is in a selection
together with water altloc B (and then so for altloc A). Therefore water
altloc B lies "over" sidechain altloc A. I had not figured that yet.
This seems to naturally make due antibumping restraints. I was about to
make some more tests, but this seems to have worked then. By the way, I
was prompted to test this way due to the comments at
strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix, which I
> 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
>> 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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