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<DIV>Dear Pavel, </DIV>
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<DIV>Thank you very much for your suggestion. </DIV>
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<DIV>I run phenix.model_vs_data model.pdb data.mtz, and the output statistics matches the one I deposited to PDB. The data should be OK. </DIV>
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<DIV>I very appreciate your help. </DIV>
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<DIV>Best wishes, </DIV>
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<DIV>Vinson</DIV>
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<B><SPAN style="FONT-WEIGHT: bold">发件人：</SPAN></B> Pavel Afonine <pafonine@lbl.gov><BR><B><SPAN style="FONT-WEIGHT: bold">收件人：</SPAN></B> PHENIX user mailing list <phenixbb@phenix-online.org><BR><B><SPAN style="FONT-WEIGHT: bold">抄 送：</SPAN></B> Vinson LIANG <lwg_conrad_1983@yahoo.com.cn><BR><B><SPAN style="FONT-WEIGHT: bold">发送日期：</SPAN></B> 2010/10/22 (周五) 12:44:58 上午<BR><B><SPAN style="FONT-WEIGHT: bold">主 题：</SPAN></B> Re: [phenixbb] R-free problem with phenix.refine<BR></FONT><BR>Hi,<BR><BR>
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<DIV>Recently I deposited a structure to PDB. However, I was told<BR></DIV><PRE>>> 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.</PRE></DIV></BLOCKQUOTE><BR>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.<BR><BR>Just run<BR><BR>phenix.model_vs_data model.pdb data.hkl <BR><BR>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.<BR><BR>
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<DIV style="FONT-FAMILY: 宋体, simsun, serif; FONT-SIZE: 12pt"><PRE>So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742.
</PRE></DIV></BLOCKQUOTE><BR>Sounds good.<BR><BR>
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<DIV style="FONT-FAMILY: 宋体, simsun, serif; FONT-SIZE: 12pt"><PRE>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.
</PRE></DIV></BLOCKQUOTE><BR>No surprises. Jumping between programs is tricky. You have to account for a lot of things to match things that different programs expect differently.<BR><BR>
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<DIV style="FONT-FAMILY: 宋体, simsun, serif; FONT-SIZE: 12pt"><PRE>Could anyone please help me to solve this problem?</PRE></DIV></BLOCKQUOTE><BR>Step-by-step:<BR><BR>1) Run<BR>phenix.model_vs_data model.pdb data.hkl <BR><BR>2) if output statistics matches the one you deposited to PDB, then you are 100% good. Come back to PDB and say this. <BR><BR>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.<BR><BR>Pavel.<BR><BR><BR></DIV></DIV></DIV></div><br>
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