<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000099">
<div class="moz-cite-prefix">Thanks Pavel.<br>
Will await the next build.<br>
<br>
<div class="moz-signature"><font color="#000099" face="Verdana"
size="2">
Thanks, <br>
Abhinav </font>
<p><font color="#000099" face="Verdana" size="2">
</font>
<font color="#0099AA" face="Verdana" size="2">
JCSG@SSRL, SLAC <br>
(650) 926-2992 <br>
</font></p>
</div>
On 06/11/2013 11:40 AM, Pavel Afonine wrote:<br>
</div>
<blockquote cite="mid:51B76F3B.4090203@lbl.gov" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">Hi Abhinav,<br>
<br>
thanks again for sending me the files off list. This let me to
identify the problem and fix it. The difference between
R-factors in phenix.refine and phenix.model_vs_data was due to a
slightly different accounting for scattering contribution from H
atoms. In both cases it was correct though. If I check in my
changes today then next available nightly build will have it
fixed.<br>
<br>
Pavel <br>
<br>
On 6/10/13 11:42 AM, Abhinav Kumar wrote:<br>
</div>
<blockquote cite="mid:51B61E2E.7010503@slac.stanford.edu"
type="cite">
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
I am getting a significant difference between the R-factors
written by phenix.refine and phenix.model_vs_data.<br>
<div class="moz-forward-container"> <br>
1. Phenix.refine <br>
phenix.refine "in.pdb" "Fobs.mtz"
"refinement.input.xray_data.labels=FP SIGFP"
"refinement.input.xray_data.high_resolution=2.50"
"fix_rotamers=True" "ordered_solvent=True"
"strategy=tls+individual_sites+individual_adp" <br>
<br>
Final R-work = 0.1829, R-free = 0.2141<br>
<br>
<br>
2. Phenix.model_vs_data<br>
phenix.model_vs_data out.pdb Fobs.mtz f_obs_label="FP"
r_free_flags_label="FreeR_flag" high_resolution=2.50
comprehensive=true<br>
<br>
r_work(re-computed) : 0.1808 <br>
r_free(re-computed) : 0.2099 <br>
<br>
How can I reproduce the phenix.refine R-factors in
phenix.model_vs_data?<br>
<br>
<div class="moz-signature">-- <br>
<font color="#000099" face="Verdana" size="2"> Thanks, <br>
Abhinav </font>
<p><font color="#000099" face="Verdana" size="2"> </font> <font
color="#0099AA" face="Verdana" size="2"> JCSG@SSRL, SLAC
<br>
(650) 926-2992 </font></p>
</div>
</div>
</blockquote>
</blockquote>
<br>
</body>
</html>