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

Dear Jack, thanks for the workaround. In my case it worked. No more unwanted NQH flips. Best, Bernhard On 12/31/2015 5:20 PM, Tanner, John J. wrote:

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: [email protected] mailto:[email protected] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html http://faculty.missouri.edu/%7Etannerjj/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 mailto:[email protected]> 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: [email protected] mailto:[email protected]

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

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- 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) 30 838-457348 Email: [email protected] Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/