[phenixbb] selective nonbonded restraint removal

Pavel Afonine PAfonine at lbl.gov
Tue Sep 4 20:41:46 PDT 2007

Hi Cathy,

sorry for probably stupid question: why you want to turn off the 
non-bonded restraints in this case?
Also, how you estimated the occupancy of TAM? Did you do one occupancy 
factor refinement per whole TAM molecule (possible option in phenix.refine)?


Cathy Lawson wrote:
> Hi Ralf,
> That is disappointing.  Lovely maps produced after a few phenix.refine 
> runs
> for a 1.6 A structure revealed an unexpected tris ligand (TAM) with 
> occupancy ~0.5.
> The density suggests that when tris is not there, 
> a side chain moves very close to that position, thus my question.
> In other regards phenix seems a great step forward in automating 
> refinement, and
> I look forward to new developments.
> best wishes,
> Cathy
>> Hi Cathy,
>> > Is it possible to turn off nonbonded restraints for particular
>> > residues/monomers, or for atoms with occupancy less than 1.0?
>> Nope, sorry. It is on the (long) to-do list.
>> BTW: each time someone asks the priority goes up.
>> Ralf
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