Re: [phenixbb] selective nonbonded restraint removal
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
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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Hi Cathy,
The density suggests that when tris is not there, a side chain moves very close to that position
You could model this with alternative conformations. If you assign "altloc" A and B to two conformers of your protein, and just, say, B to your TAM, then the ligand would only "see" your B protein. If you don't define the B conformer (no atoms) then TAM wouldn't see that part of the protein at all. Actually, this approach seems better to me than working with atom selections. Ralf
Hi Cathy,
You may have tried this already but if not, at this resolution and for the particular problem you mention (ligand and side chain competing for the same site) I highly recommend Shelxl. It deals with such problems like a charm.
Cheers,
Boaz
----- Original Message -----
From: Cathy Lawson
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
Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
participants (4)
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Boaz Shaanan -
Cathy Lawson -
Pavel Afonine -
Ralf W. Grosse-Kunstleve