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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 <[log in to unmask]> > 收件人： PHENIX user mailing list <[log in to unmask]> > 抄 送： Vinson LIANG <[log in to unmask]> > 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. > > > > > > > > > > > > > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A