[phenixbb] Selection of R-free set for twin refinement
Peter Zwart
phzwart at gmail.com
Thu May 7 10:17:20 PDT 2009
No twin law is needed for rfree flags: it uses the lattice symmetry
from the unit cell for this purpose (which includes the twin law you
gave)
Adding the twin law only activates the use of the twin target.
P
2009/5/7 Boaz Shaanan <bshaanan at bgu.ac.il>:
> 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
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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
>> >> 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
> _______________________________________________
> 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
CCTBX: http://cctbx.sf.net
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