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

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 Date: Thursday, May 7, 2009 0:08 Subject: Re: [phenixbb] Selection of R-free set for twin refinement To: PHENIX user mailing list

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

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Hi Peter,

I went ahead and tried your suggestion in phenix.refine. With

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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

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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 Date: Wednesday, May 6, 2009 17:52 Subject: Re: [phenixbb] Selection of R-free set for twin refinement To: PHENIX user mailing list

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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

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Hi,

If I understand correctly, the Phenix manual suggests two

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selecting the R-free set for twin refinement. One is to do

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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

2009/5/6 Boaz Shaanan : options for this using the possible in

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conjunction with twin refinement.

     Thanks,

                Boaz

----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 5, 2009 4:53 Subject: Re: [phenixbb] ncs To: PHENIX user mailing list

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I see. I suggest to run two refinements:

- with NCS and "optimize_wxc=true optimize_wxu=true"

2009/5/6 Boaz Shaanan : this parameter previous message, options, and

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- 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:

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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

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turned

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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 >> [email protected] >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> > _______________________________________________ > phenixbb mailing list > [email protected] > http://www.phenix-online.org/mailman/listinfo/phenixbb > > >

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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 [email protected] 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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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 [email protected] 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