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

Wed May 6 12:54:41 PDT 2009

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
> >> >>> _______________________________________________
> >> >>> phenixbb mailing list
> >> >>> phenixbb at phenix-online.org
> >> >>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >> >>>
> >> >>>
> >> >>>
> >> >> _______________________________________________
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> >> >>
> >> >>
> >> >>
> >> >
> >> > _______________________________________________
> >> > phenixbb mailing list
> >> > phenixbb at phenix-online.org
> >> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >> >
> >>
> >
> > 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
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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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