I must note that it is also interesting to know why the sfcheck produced the R-factor that is twice as high. Of course, the R/Rfree are not supposed to match precisely (as I recall, sfcheck uses Babinet bulk solvent correction which is presumably inferior to the mask-based approach), but 28.6 versus 14.7? Something may be seriously wrong.
On Fri, 2010-10-22 at 09:37 +0200, Tim Gruene wrote: > Dear Vinson, > > I would still be interested about what was the cause of the missing R-free > flags > and how you resolved it (I hope I did not miss an email). > > Kind regards, Tim > > On Fri, Oct 22, 2010 at 02:33:03PM +0800, Vinson LIANG wrote: > > > > > > Dear all, > > > > > > > > > > Thank you very much for your suggestions. > > > > I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data > > would be enough for PDB. > > > > > > Best wishes, > > > > Vinson > > > > > > > > > > > > > > > > > > 发件人： Pavel Afonine <pafon...@lbl.gov> > > 收件人： PHENIX user mailing list <pheni...@phenix-online.org> > > 抄 送： Vinson LIANG <lwg_conrad_1...@yahoo.com.cn> > > 发送日期： 2010/10/22 (周五) 12:44:58 上午 > > 主 题： Re: [phenixbb] R-free problem with phenix.refine > > > > Hi, > > > > > > > > > > Recently I deposited a structure to PDB. However, I was told > > >> The R value of SF check are different from your reported value. > > >> > > >> R work in SF check = 0.2859 > > >> your reported R work = 0.1474 > > >> Also there are no R free flags in your sending files, but you reported R > > >> free value in your all deposition. > > well, SF check is not the best tool to check things - it's not just my only > > vision, see lots of conversations on this topic on bb. > > > > Just run > > > > phenix.model_vs_data model.pdb data.hkl > > > > and if output statistics matches the one you deposited to PDB, then you are > > 100% good. If it doesn't match then there is something to worry about. > > > > > > > > So, I rerun my deposited file with phenix.refine, and it gave a > > R-work=0.1475, R-free=0.1742. > > > > Sounds good. > > > > > > > > However, when I tried to run the same file with refmac5, error came with > > "Free R label has not been set". I guess phenix.refine gives Rree-R label > > that other program could not recognize. > > > > No surprises. Jumping between programs is tricky. You have to account for a > > lot of things to match things that different programs expect differently. > > > > > > > > Could anyone please help me to solve this problem? > > Step-by-step: > > > > 1) Run > > phenix.model_vs_data model.pdb data.hkl > > > > 2) if output statistics matches the one you deposited to PDB, then you are > > 100% good. Come back to PDB and say this. > > > > 3) If it doesn't match then there is something that you need to fix. If you > > can't fix or have no idea what's wrong, you can send me the data and model > > and I will have a look. > > > > Pavel. > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
