<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Pavel,</div><div> </div><div>It looks work. But for the refined PDB, it seems it was in read-only format, which I cannot copy. For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB, am I right?</div><div> </div><div>Smith<br><br><br><br></div><div style="position: relative; zoom: 1;"></div><div id="divNeteaseMailCard"></div><div><br></div><div id="isForwardContent">-------- Forwarding messages --------<br>From: "Pavel Afonine" <pafonine@lbl.gov><br>Date: 2015-05-21 14:44:30<br>To: "Smith Liu" <smith_liu123@163.com>,phenixbb@phenix-online.org<br>Subject: Re: [phenixbb] on B-factor refine of the phenix.real_space_refine<br>
<br>
<blockquote cite="mid:2232f6a7.9166.14d7513b719.Coremail.smith_liu123@163.com" type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;">
<div>I have a EM map (.mrc), with fitting and based on a crystal
structure I got the fitted PDB file. I convert the mrc map to
the CCP4 map�� </div>
</div>
</blockquote>
<br>
no need to convert .mrc into .ccp4 (isn't it the same thing?).
Anyways, phenix.real_space_refine can use both.<br>
<br>
<blockquote cite="mid:2232f6a7.9166.14d7513b719.Coremail.smith_liu123@163.com" type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;">
<div>and I run phenix.real_space_refine model.pdb map.mtz
run=adp, with phenix-dev-2034, in order to get my own
b-factors for my fitted PDB based on my EM map. However after
the above phenix.real_space_refine, I checked the refined PDB,
and I find phenix.real_space_refine neither change the
coordinates, nor change the b-factors for each atom.</div>
</div>
</blockquote>
<br>
I need to see the files to be able to comment. If you share the
files (off list and not sending directly via email but using things
like Dropbox instead) then I will be happy to have a look.<br>
<br>
<blockquote cite="mid:2232f6a7.9166.14d7513b719.Coremail.smith_liu123@163.com" type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;">
<div> Thus will you please introduce to me how can I get my own
b-factors for my fitted PDB in order to deposit my map and
fitte pdb to the EM database?<br>
</div>
</div>
</blockquote>
<br>
phenix.real_space_refine model.pdb map.mtz run=adp<br>
<br>
should just do what you want. If it didn't - see above (I need to
see the files).<br>
<br>
Pavel<br>
<br>
</div></div><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>