Hi Peter,<br><br>As far as I can see (by comparing the input & output mtz files) this command: <br><br>phenix.refine H1pk.mtz H1pk.pdb xray_data.r_free_flags.generate=True twin_law="-k,-h,-l"<br><br>does generate a new set of R-free reflections in the newly generated mtz file, hopefully taking into account the twin law.<br>
<br> Cheers,<br><br> Boaz<br>----<br><br><br>----- Original Message -----<br>From: Peter Zwart <phzwart@gmail.com><br>Date: Thursday, May 7, 2009 0:08<br>Subject: Re: [phenixbb] Selection of R-free set for twin refinement<br>To: PHENIX user mailing list <phenixbb@phenix-online.org><br><br>> Okai,<br>> <br>> when the twin law is not specified, it will not do a twin based<br>> refinement, but does take all possible twin laws into considerations<br>> when making an free set.<br>> <br>> when specifying the twin law, a twin based refinement is carried out.<br>> <br>> I am not sure about making a new test set when you already have one.<br>> Pavel, Ralf, any clue?<br>> <br>> P<br>> <br>> <br>> 2009/5/6 Boaz Shaanan <bshaanan@bgu.ac.il>:<br>> > Hi Peter,<br>> ><br>> > I went ahead and tried your suggestion in phenix.refine. With <br>> this parameter<br>> > in the command line<br>> ><br>> > xray_data.r_free_flags.generate=True<br>> ><br>> > but without twin_law="whatever" parameter, the program does <br>> not have any<br>> > clue about twinning and the refinement indeed ignores it, at <br>> least by the<br>> > look of the progress (I didn't let it go to the end and then <br>> check the<br>> > resulting mtz file). On the other hand, with <br>> twin_law="whatever" all is OK.<br>> > In fact I also got an answer to my second question in the <br>> previous message,<br>> > i.e. that a new R-free set is selected even thought the <br>> incoming mtz file<br>> > had a previously selected R-free set (by scala). I guess I <br>> should use the<br>> > new mtz file from now on and not use <br>> xray_data.r_free_flags.generate=True> anymore, is this correct ?<br>> ><br>> > Cheers,<br>> ><br>> > Boaz<br>> > ----- Original Message -----<br>> > From: Peter Zwart <phzwart@gmail.com><br>> > Date: Wednesday, May 6, 2009 17:52<br>> > Subject: Re: [phenixbb] Selection of R-free set for twin refinement<br>> > To: PHENIX user mailing list <phenixbb@phenix-online.org><br>> ><br>> >> Hi Boaz,<br>> >><br>> >> The two options are equivalent and no twin law needs to be <br>> specified>> in either case.<br>> >><br>> >> SA should be possible with twin refinement.<br>> >><br>> >> Cheers<br>> >><br>> >> Peter<br>> >><br>> >> 2009/5/6 Boaz Shaanan <bshaanan@bgu.ac.il>:<br>> >> > Hi,<br>> >> ><br>> >> > If I understand correctly, the Phenix manual suggests two<br>> >> options for<br>> >> > selecting the R-free set for twin refinement. One is to do<br>> >> this using the<br>> >> > phenix.reflection_file_converter with the parameter<br>> >> ><br>> >> > --use-lattice-symmetry-in-r-free-flag-generation<br>> >> ><br>> >> > which I suppose does not require input of the twin law. The<br>> >> second is in the<br>> >> > actual refinement using the parameter<br>> >> ><br>> >> > xray_data.r_free_flags.generate=True<br>> >> ><br>> >> > in which case the twin law is part of the input. My first<br>> >> question is<br>> >> > whether the two options<br>> >> > are truly equivalent. The second question is whether one can<br>> >> go into either<br>> >> > of them with an mtz file<br>> >> > in which R-free set reflections have already been selected<br>> >> (e.g. in scala or<br>> >> > XDS) without<br>> >> > any twinning assumption, or should one use a file without any<br>> >> R-free set<br>> >> > altogether and let the<br>> >> > phenix script choose it from scratch, under the twinning <br>> assumption.>> ><br>> >> > Another (related) question is whether simulated annealing is<br>> >> possible in<br>> >> > conjunction with<br>> >> > twin refinement.<br>> >> ><br>> >> > Thanks,<br>> >> ><br>> >> > Boaz<br>> >> ><br>> >> ><br>> >> > ----- Original Message -----<br>> >> > From: Pavel Afonine <PAfonine@lbl.gov><br>> >> > Date: Tuesday, May 5, 2009 4:53<br>> >> > Subject: Re: [phenixbb] ncs<br>> >> > To: PHENIX user mailing list <phenixbb@phenix-online.org><br>> >> ><br>> >> >> I see. I suggest to run two refinements:<br>> >> >><br>> >> >> - with NCS and "optimize_wxc=true optimize_wxu=true" <br>> options, and<br>> >> >><br>> >> >> - without NCS and with "optimize_wxc=true optimize_wxu=true".<br>> >> >><br>> >> >> This will make it weight-choice independent and so easier to<br>> >> >> understand.<br>> >> >> Otherwise, since NCS term is included in weights calculation,<br>> >> >> using or<br>> >> >> not using NCS may change the X-ray/Restrains weight which may<br>> >> >> have<br>> >> >> larger effects than using/not using NCS itself.<br>> >> >><br>> >> >> Pavel.<br>> >> >><br>> >> >><br>> >> >> On 5/4/09 6:48 PM, Maia Cherney wrote:<br>> >> >> > Hi Pavel,<br>> >> >> > The resolution is 2.15 A. The NCS was always on during the<br>> >> >> refinement<br>> >> >> > until we got low R factors (19.2% and 21.2%). Then the <br>> NCS was<br>> >> >> turned<br>> >> >> > off for the final refinement and the R factors increased,<br>> >> >> which is<br>> >> >> > strange as they should be going down when you apply less<br>> >> >> restraints.<br>> >> >> > There are five restraint groups in the asym. unit.<br>> >> >> ><br>> >> >> > Maia<br>> >> >> ><br>> >> >> ><br>> >> >> ><br>> >> >> > Pavel Afonine wrote:<br>> >> >> ><br>> >> >> >> Hi Maia,<br>> >> >> >><br>> >> >> >> - I'm wondering why this puzzles you?<br>> >> >> >><br>> >> >> >> - The gap Rfree-Rwork seems suspiciously small, <br>> although I<br>> >> >> can't tell<br>> >> >> >> without knowing the resolution.<br>> >> >> >><br>> >> >> >> - Overall, better R-factors (Rwork, Rfree and Rfree-Rwork)<br>> >> >> mean that<br>> >> >> >> among many possible refinement strategies you have <br>> chosen the<br>> >> >> one that<br>> >> >> >> is better than the others.<br>> >> >> >><br>> >> >> >> What is the resolution?<br>> >> >> >> What are the R-factor before using NCS?<br>> >> >> >> What will be the R-factors after you turn NCS back off?<br>> >> >> >><br>> >> >> >> Pavel.<br>> >> >> >><br>> >> >> >><br>> >> >> >> On 5/4/09 12:27 PM, Maia Cherney wrote:<br>> >> >> >><br>> >> >> >><br>> >> >> >>> Hi everybody,<br>> >> >> >>> I am wondering why my final structure refined with NCS=True<br>> >> >> has lower R<br>> >> >> >>> factors (19.2% and 21.2%) than without NCS by<br>> >> approximately 1.5%.<br>> >> >> >>><br>> >> >> >>> Leo<br>> >> >> >>> _______________________________________________<br>> >> >> >>> phenixbb mailing list<br>> >> >> >>> phenixbb@phenix-online.org<br>> >> >> >>> http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> >> >> >>><br>> >> >> >>><br>> >> >> >>><br>> >> >> >> _______________________________________________<br>> >> >> >> phenixbb mailing list<br>> >> >> >> phenixbb@phenix-online.org<br>> >> >> >> http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> >> >> >><br>> >> >> >><br>> >> >> >><br>> >> >> ><br>> >> >> > _______________________________________________<br>> >> >> > phenixbb mailing list<br>> >> >> > phenixbb@phenix-online.org<br>> >> >> > http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> >> >> ><br>> >> >><br>> >> ><br>> >> > Boaz Shaanan, Ph.D.<br>> >> > Dept. of Life Sciences<br>> >> > Ben-Gurion University of the Negev<br>> >> > Beer-Sheva 84105<br>> >> > Israel<br>> >> > Phone: 972-8-647-2220 ; Fax: 646-1710<br>> >> > Skype: boaz.shaanan<br>> >> > _______________________________________________<br>> >> > phenixbb mailing list<br>> >> > phenixbb@phenix-online.org<br>> >> > http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> >> ><br>> >> ><br>> >><br>> >><br>> >><br>> >> --<br>> >> --------------------------------------------------------------<br>> ---<br>> >> P.H. Zwart<br>> >> Beamline Scientist<br>> >> Berkeley Center for Structural Biology<br>> >> Lawrence Berkeley National Laboratories<br>> >> 1 Cyclotron Road, Berkeley, CA-94703, USA<br>> >> Cell: 510 289 9246<br>> >> BCSB: http://bcsb.als.lbl.gov<br>> >> PHENIX: http://www.phenix-online.org<br>> >> CCTBX: http://cctbx.sf.net<br>> >> --------------------------------------------------------------<br>> ---<br>> >><br>> >> _______________________________________________<br>> >> phenixbb mailing list<br>> >> phenixbb@phenix-online.org<br>> >> http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> >><br>> ><br>> > Boaz Shaanan, Ph.D.<br>> > Dept. of Life Sciences<br>> > Ben-Gurion University of the Negev<br>> > Beer-Sheva 84105<br>> > Israel<br>> > Phone: 972-8-647-2220 ; Fax: 646-1710<br>> > Skype: boaz.shaanan<br>> > _______________________________________________<br>> > phenixbb mailing list<br>> > phenixbb@phenix-online.org<br>> > http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> ><br>> ><br>> <br>> <br>> <br>> -- <br>> -----------------------------------------------------------------<br>> P.H. Zwart<br>> Beamline Scientist<br>> Berkeley Center for Structural Biology<br>> Lawrence Berkeley National Laboratories<br>> 1 Cyclotron Road, Berkeley, CA-94703, USA<br>> Cell: 510 289 9246<br>> BCSB: http://bcsb.als.lbl.gov<br>> PHENIX: http://www.phenix-online.org<br>> CCTBX: http://cctbx.sf.net<br>> -----------------------------------------------------------------<br>> <br>> _______________________________________________<br>> phenixbb mailing list<br>> phenixbb@phenix-online.org<br>> http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> <BR><BR>Boaz Shaanan, Ph.D.<br>Dept. of Life Sciences<br>Ben-Gurion University of the Negev<br>Beer-Sheva 84105<br>Israel<br>Phone: 972-8-647-2220 ; Fax: 646-1710<br>Skype: boaz.shaanan</BR></BR>