[phenixbb] Selection of R-free set for twin refinement
Boaz Shaanan
bshaanan at bgu.ac.il
Thu May 7 09:07:55 PDT 2009
Hi Peter,
As far as I can see (by comparing the input & output mtz files) this command:
phenix.refine H1pk.mtz H1pk.pdb xray_data.r_free_flags.generate=True twin_law="-k,-h,-l"
does generate a new set of R-free reflections in the newly generated mtz file, hopefully taking into account the twin law.
Cheers,
Boaz
----
----- Original Message -----
From: Peter Zwart <phzwart at gmail.com>
Date: Thursday, May 7, 2009 0:08
Subject: Re: [phenixbb] Selection of R-free set for twin refinement
To: PHENIX user mailing list <phenixbb at phenix-online.org>
> 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
> >> >> >>> _______________________________________________
> >> >> >>> phenixbb mailing list
> >> >> >>> phenixbb at phenix-online.org
> >> >> >>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >> _______________________________________________
> >> >> >> phenixbb mailing list
> >> >> >> phenixbb at phenix-online.org
> >> >> >> http://www.phenix-online.org/mailman/listinfo/phenixbb
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >
> >> >> > _______________________________________________
> >> >> > 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
> >> CCTBX: http://cctbx.sf.net
> >> --------------------------------------------------------------
> ---
> >>
> >> _______________________________________________
> >> 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
> CCTBX: http://cctbx.sf.net
> -----------------------------------------------------------------
>
> _______________________________________________
> 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
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