[phenixbb] alternate side chains conjugated with water molecules

Jorge Iulek iulek at uepg.br
Sun May 31 04:59:13 PDT 2015

Dear Pavel,

     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 
found later.


> 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.
> Pavel
> 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