[phenixbb] unwanted N/Q/H flipping in PHENIX.REFINE

[Tanner, John J.]

Bernard,

I have experienced this problem too.  A workaround is to disable both NQH flips and real space refinement.

    strategy = *individual_sites individual_sites_real_space rigid_body \
               *individual_adp group_adp *tls occupancies group_anomalous


Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On Dec 29, 2015, at 11:57 AM, Pavel Afonine <pafonine at lbl.gov<mailto:pafonine at lbl.gov>> wrote:

Hi Bernhard,

If you disable the flips they should not happen during refinement.
This is something that I heard before but users were reluctant to provide evidence.
Could you please send me data file, and two PDB files (before and after refinement) and indicate residues that are undesirably flipped? In case there are ligands, please send ligand CIF files too.
Once I have files I will run refinement myself and see how this behavior may be prevented.

Thanks,
Pavel


On 12/29/15 09:38, Bernhard Loll wrote:
Dear all,

I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155.

The problem I am facing is the following:

Running the Molprobity server, it suggests me to correct a couple of N/Q/H
flips. I perform the flips re-run PHENIX.REFINE with  “Automatically
correct N/Q/H  errors” not ticked. The log file confirms the selection
with nqh_flips = False.

Nevertheless PHENIX.REFINE again flips these residues and the output PDB
file has all previously flipped residues “re-flipped” in comparison to the
input PDB file. I am very confident that the automatically flips performed
by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding
sites.

Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips
were set to false?

Any help is appreciated.

Cheers,

Bernhard


Dr. Bernhard Loll
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fuer Chemie und Biochemie
AG Strukturbiochemie
Takustr. 6
D-14195 Berlin
Germany

Phone: +49 (0) 30 838-57348
Fax:   +49 (0) 30 838-454936
Email: loll at chemie.fu-berlin.de<mailto:loll at chemie.fu-berlin.de>

Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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