<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Jianghai,<br>
<br>
I see several possibilities to think about or/and try out:<br>
<br>
1) Fix the coordinates of atoms in the domains for which the high
resolution structure is available and refine the rest;<br>
2) Refine the domains for which the high resolution structure is
available as rigid bodies and for the rest refine individual parameters;<br>
3) There is no specific option in phenix.refine to restrain the
secondary structure elements, however there is a tedious way of doing
this (according to Ralf) by defining custom bonds and angles between
specific atoms forming the secondary structure motifs. Look "Definition
of custom bonds and angles" in the latest CCI Apps phenix.refine
documentation for technical details. <br>
<br>
You can perform "1)" and "2)" in ONE refinement run by combining
several refinement strategies and using specific selections for
refinable parameters.<br>
<br>
Overall, at 3.8A resolution the refinement of individual atomic
parameters (coordinates, B-factors) is questionable. I would consider
to try to refine group parameters for B-factors (trough TLS or/and
group B (like one B per residue)) and try to switch between rigid body
refinement of smaller fragments of your model and refinement individual
positional parameters or mix of individual and rigid body refinement.<br>
<br>
Also, I will think about making a specific option for automatic
generation of secondary structure restrains. However, given the amount
of work it may require this option will not appear in near future.<br>
<br>
Pavel.<br>
<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="mid996D241F-7BD1-4EA6-A02D-2B430626BBDF@cbr.med.harvard.edu"
type="cite">Hi all,
<div><br class="khtml-block-placeholder">
</div>
<div>I am refining a low resolution structure (~3.8 A). For some of
the domains in the structure, we already have high resolution
structures. Despite of some conformational changes in some loops, the
core structures should be the same. I am wondering if it is possible
to restrain the secondary structures in phenix.refine.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Thanks.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<div><br>
<div> <span class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div>+++++++++++++++++++++++++++++++</div>
<div>Jianghai Zhu, Ph.D</div>
<div>CBR Institute for Biomedical Research</div>
<div>Department of Pathology</div>
<div>Harvard Medical School</div>
<div>200 Longwood Ave., Boston, MA 02115</div>
<div>Ph: 617-278-3211</div>
<div>Fx: 618-278-3232</div>
<div>+++++++++++++++++++++++++++++++</div>
<div><br class="khtml-block-placeholder">
</div>
<br class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
</div>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>