[phenixbb] alternate side chains conjugated with water molecules

Jorge Iulek iulek at uepg.br
Sat May 16 13:29:18 PDT 2015

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:


     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.


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