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

[Bernhard Loll]

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: tannerjj at missouri.edu <mailto:tannerjj at missouri.edu>
> 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 <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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-- 
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: loll at chemie.fu-berlin.de
Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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