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)? Thanks! Pavel. 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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