<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
B-factor refinement does refine B-factors (change B-factors) and
coordinate refinement does refine coordinates (change coordinates).
In turn, B-factor refinement does not change coordinates, and
coordinate refinement does not change B-factors. And if you do both,
then coordinates and B-factors will be changed, obviously.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/12/15 19:18, Smith Lee wrote:<br>
</div>
<blockquote
cite="mid:1052622217.2109906.1439432330060.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yui_3_16_0_1_1439430627599_3035"> Dear All,</div>
<div id="yui_3_16_0_1_1439430627599_3101"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3071" dir="ltr">I first run
a default phenix.real_space_refine with the map and initial
model, with the model got, I run phenix.real_space_refine�
with run=adp, I find for the second phenix.real_space_refine
step with run=adp, it can gives a reasonable value of
b-factors for each residues in the model, and it cannot modify
the coordinates of any atoms in the model (in comparison with
the model got by the default phenix.real_space_refine in the
first step).</div>
<div id="yui_3_16_0_1_1439430627599_3291" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3290" dir="ltr">I just
read�a Nature paper from David Baker group "Atomic-accuracy
models from 4.5-� cryo-electron microscopy data with
density-guided iterative local refinement", it says "<font
id="yui_3_16_0_1_1439430627599_3212" size="2">Because
cryo-EM maps are frequently better in resolution in some
regions than others, atomic </font><i
id="yui_3_16_0_1_1439430627599_3213"><font
id="yui_3_16_0_1_1439430627599_3214" face="Minion
Pro,Minion Pro" size="2"><font
id="yui_3_16_0_1_1439430627599_3215" face="Minion
Pro,Minion Pro" size="2">B </font></font></i><font
id="yui_3_16_0_1_1439430627599_3216" size="2">factors are
fit against cryo-EM density data to maximize the real-space
correlation between model and map".</font></div>
<div id="yui_3_16_0_1_1439430627599_3318" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3319" dir="ltr"><br>
</div>
<font id="yui_3_16_0_1_1439430627599_3325" size="2">
<div id="yui_3_16_0_1_1439430627599_3319" dir="ltr">For <font
id="yui_3_16_0_1_1439430627599_3331" size="2">Real-space </font><i
id="yui_3_16_0_1_1439430627599_3332"><font
id="yui_3_16_0_1_1439430627599_3333" face="Minion
Pro,Minion Pro" size="2"><font
id="yui_3_16_0_1_1439430627599_3334" face="Minion
Pro,Minion Pro" size="2">B</font></font></i><font
id="yui_3_16_0_1_1439430627599_3335" size="2">-factor
refinement, the math functions used by that Nature paper
include,</font></div>
<div id="yui_3_16_0_1_1439430627599_3369" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3355" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3319" dir="ltr">�<br>
</div>
<div id="yui_3_16_0_1_1439430627599_3382" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3383" dir="ltr">( <i
id="yui_3_16_0_1_1439430627599_3384">f</i> is a scattering
factor fit to each element)</div>
<div id="yui_3_16_0_1_1439430627599_3395" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3394" dir="ltr"><br>
</div>
</font>
<div id="yui_3_16_0_1_1439430627599_3319" dir="ltr">�<br>
</div>
<div id="yui_3_16_0_1_1439430627599_3405" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3406" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3407" dir="ltr"><br>
�</div>
<div id="yui_3_16_0_1_1439430627599_3419" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3420" dir="ltr"><br>
�</div>
<div id="yui_3_16_0_1_1439430627599_3422" dir="ltr"><br>
�</div>
<div id="yui_3_16_0_1_1439430627599_3464" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3423" dir="ltr">My question
is, does b-factor refine only give a reasonable b-factor to
each atom or residue �in the model (so that we know the
displacement of each atom or residue), or besides giving
reasonable b-factor, it can also change and optimize the x y z
coordinates of each atom in the model, and the� phenomenon I
observed in phenix.real_space_refine on that it only gives
reasonable b-factor without modification of the x y z
coordinates was only limited to the case I see in
phenix.real_space_refine? </div>
<div id="yui_3_16_0_1_1439430627599_3534" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3536" dir="ltr">Best
regards.</div>
<div id="yui_3_16_0_1_1439430627599_3535" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1439430627599_3545" dir="ltr">Smith<br>
</div>
</div>
</blockquote>
<br>
</body>
</html>