<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=GB2312" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi,<br>
<br>
<blockquote cite="mid:875493.52298.qm@web15302.mail.cnb.yahoo.com"
type="cite">
<style type="text/css"><!-- DIV {margin:0px;} --></style>
<div style="font-family: ËÎÌå,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 cite="mid:875493.52298.qm@web15302.mail.cnb.yahoo.com"
type="cite">
<div style="font-family: ËÎÌå,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 cite="mid:875493.52298.qm@web15302.mail.cnb.yahoo.com"
type="cite">
<div style="font-family: ËÎÌå,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 cite="mid:875493.52298.qm@web15302.mail.cnb.yahoo.com"
type="cite">
<div style="font-family: ËÎÌå,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>
</body>
</html>