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Hi Vinson,<br>
<br>
so, this means that your data and model are ok, and the statistics
is consistent. Meaning that what you have reported in your PDB file
header (R-factors, and so on) are correct and correspond to the
data. Great! Then you should go back to PDB and explain this.<br>
<br>
Reference to phenix.model_vs_data is:<br>
<br>
Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW,
Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD:<br>
phenix.model_vs_data: a high-level tool for the calculation of
crystallographic model and data statistics<br>
J. Appl. Cryst. 2010, 43, 669-676.<br>
<br>
Good luck and let us know if you have any other problems or
questions!<br>
Pavel.<br>
<br>
<br>
On 10/21/10 11:21 PM, Vinson LIANG wrote:
<blockquote cite="mid:245527.51301.qm@web15307.mail.cnb.yahoo.com"
type="cite">
<style type="text/css"><!-- DIV {margin:0px;} --></style>
<div style="font-family: 宋体,simsun,serif; font-size: 12pt;">
<div>Dear Pavel, </div>
<div> </div>
<div>Thank you very much for your suggestion. </div>
<div> </div>
<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>
<div> </div>
<div>I very appreciate your help. </div>
<div> </div>
<div>Best wishes, </div>
<div> </div>
<div>Vinson</div>
<div> </div>
<div><br>
</div>
<div>
<div style="font-family: 宋体,simsun,serif; font-size: 12pt;"><br>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><font face="Tahoma"
size="2">
<hr size="1">
<b><span style="font-weight: bold;">发件人：</span></b>
Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a><br>
<b><span style="font-weight: bold;">收件人：</span></b>
PHENIX user mailing list
<a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a><br>
<b><span style="font-weight: bold;">抄 送：</span></b>
Vinson LIANG <a class="moz-txt-link-rfc2396E" href="mailto:lwg_conrad_1983@yahoo.com.cn"><lwg_conrad_1983@yahoo.com.cn></a><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>
<blockquote type="cite">
<div style="font-family: 宋体,simsun,serif; font-size:
12pt;">
<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>
<blockquote type="cite">
<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>
<blockquote type="cite">
<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>
<blockquote type="cite">
<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>
<pre wrap="">
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</pre>
</blockquote>
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