[phenixbb] Selection of R-free set for twin refinement

Peter Zwart phzwart at gmail.com
Wed May 6 07:52:18 PDT 2009


Hi Boaz,

The two options are equivalent and no twin law needs to be specified
in either case.

SA should be possible with twin refinement.

Cheers

Peter

2009/5/6 Boaz Shaanan <bshaanan at bgu.ac.il>:
> Hi,
>
> If I understand correctly, the Phenix manual suggests two options for
> selecting the R-free set for twin refinement. One is to do this using the
> phenix.reflection_file_converter with the parameter
>
> --use-lattice-symmetry-in-r-free-flag-generation
>
> which I suppose does not require input of the twin law. The second is in the
> actual refinement using the parameter
>
> xray_data.r_free_flags.generate=True
>
> in which case the twin law is part of the input. My first question is
> whether the two options
> are truly equivalent. The second question is whether one can go into either
> of them with an mtz file
> in which R-free set reflections have already been selected (e.g. in scala or
> XDS) without
> any twinning assumption, or should one use a file without any R-free set
> altogether and let the
> phenix script choose it from scratch, under the twinning assumption.
>
> Another (related) question is whether simulated annealing is possible in
> conjunction with
> twin refinement.
>
>     Thanks,
>
>                Boaz
>
>
> ----- Original Message -----
> From: Pavel Afonine <PAfonine at lbl.gov>
> Date: Tuesday, May 5, 2009 4:53
> Subject: Re: [phenixbb] ncs
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
>> I see. I suggest to run two refinements:
>>
>> - with NCS and "optimize_wxc=true optimize_wxu=true" options, and
>>
>> - without NCS and with "optimize_wxc=true optimize_wxu=true".
>>
>> This will make it weight-choice independent and so easier to
>> understand.
>> Otherwise, since NCS term is included in weights calculation,
>> using or
>> not using NCS may change the X-ray/Restrains weight which may
>> have
>> larger effects than using/not using NCS itself.
>>
>> Pavel.
>>
>>
>> On 5/4/09 6:48 PM, Maia Cherney wrote:
>> > Hi Pavel,
>> > The resolution is 2.15 A. The NCS was always on during the
>> refinement
>> > until we got low R factors (19.2% and 21.2%). Then the NCS was
>> turned
>> > off for the final refinement and the R factors increased,
>> which is
>> > strange as they should be going down when you apply less
>> restraints.
>> > There are five restraint groups in the asym. unit.
>> >
>> > Maia
>> >
>> >
>> >
>> > Pavel Afonine wrote:
>> >
>> >> Hi Maia,
>> >>
>> >> - I'm wondering why this puzzles you?
>> >>
>> >> - The gap Rfree-Rwork seems suspiciously small, although I
>> can't tell
>> >> without knowing the resolution.
>> >>
>> >> - Overall, better R-factors (Rwork, Rfree and Rfree-Rwork)
>> mean that
>> >> among many possible refinement strategies you have chosen the
>> one that
>> >> is better than the others.
>> >>
>> >> What is the resolution?
>> >> What are the R-factor  before using NCS?
>> >> What will be the R-factors after you turn NCS back off?
>> >>
>> >> Pavel.
>> >>
>> >>
>> >> On 5/4/09 12:27 PM, Maia Cherney wrote:
>> >>
>> >>
>> >>> Hi everybody,
>> >>> I am wondering why my final structure refined with NCS=True
>> has lower  R
>> >>> factors (19.2% and 21.2%) than without NCS by approximately 1.5%.
>> >>>
>> >>> Leo
>> >>> _______________________________________________
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>> >>>
>> >>>
>> >>>
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>> >>
>> >>
>> >
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>> >
>>
>
> 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
> _______________________________________________
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> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>



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