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

Peter Zwart phzwart at gmail.com
Wed May 6 14:07:52 PDT 2009


Okai,

when the twin law is not specified, it will not do a twin based
refinement, but does take all possible twin laws into considerations
when making an free set.

when specifying the twin law, a twin based refinement is carried out.

I am not sure about making a new test set when you already have one.
Pavel, Ralf, any clue?

P


2009/5/6 Boaz Shaanan <bshaanan at bgu.ac.il>:
> Hi Peter,
>
> I went ahead and tried your suggestion in phenix.refine. With this parameter
> in the command line
>
> xray_data.r_free_flags.generate=True
>
>  but without twin_law="whatever" parameter, the program does not have any
> clue about twinning and the refinement indeed ignores it, at least by the
> look of the progress (I didn't let it go to the end and then check the
> resulting mtz file). On the other hand, with twin_law="whatever" all is OK.
> In fact I also got an answer to my second question in the previous message,
> i.e. that a new R-free set is selected even thought the incoming mtz file
> had a previously selected R-free set (by scala). I guess I should use the
> new mtz file from now on and not use xray_data.r_free_flags.generate=True
> anymore, is this correct ?
>
>  Cheers,
>
>              Boaz
> ----- Original Message -----
> From: Peter Zwart <phzwart at gmail.com>
> Date: Wednesday, May 6, 2009 17:52
> Subject: Re: [phenixbb] Selection of R-free set for twin refinement
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
>> 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
>> > _______________________________________________
>> > phenixbb mailing list
>> > phenixbb at phenix-online.org
>> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>> >
>> >
>>
>>
>>
>> --
>> -----------------------------------------------------------------
>> P.H. Zwart
>> Beamline Scientist
>> Berkeley Center for Structural Biology
>> Lawrence Berkeley National Laboratories
>> 1 Cyclotron Road, Berkeley, CA-94703, USA
>> Cell: 510 289 9246
>> BCSB:     http://bcsb.als.lbl.gov
>> PHENIX: http://www.phenix-online.org
>> CCTBX:  http://cctbx.sf.net
>> -----------------------------------------------------------------
>>
>> _______________________________________________
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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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>



-- 
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:     http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
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