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Hi Pascal,<br>
<br>
it's not automated yet, but you can do it manually. In phenix.refine
you can define "custom bonds" and "custom angles". So in your case you
can just define such kind of pseudo-bonds between atom pairs that
stabilize the secondary structure. <br>
<br>
Look the manual for more informations:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/refinement.htm">http://phenix-online.org/documentation/refinement.htm</a><br>
<br>
Please let me know if you have any questions!<br>
Pavel.<br>
<br>
<br>
On 6/4/2008 2:29 PM, Pascal EGEA wrote:
<blockquote cite="mid:9DDCE28D-4FB2-43F6-83A7-A76591229CA9@msg.ucsf.edu"
type="cite">Dear All,<br>
<div><br>
</div>
<div>I am currently refining a structure at moderate resolution
(~3.4A) which is mainly composed of alpha-helices . Is there a way to
constrain the backbone geometry of the alpha helical regions in the
model used for refinement.</div>
<div>Many Thanks,</div>
<div><br>
</div>
<div>
<div> <span class="Apple-style-span"
style="border-collapse: separate; 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; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; 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; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<div>
<div>
<div>Pascal F. Egea, PhD</div>
<div>Post Doctoral Researcher</div>
<div>University of California San Francisco</div>
<div>Department of Biophysics and Biochemistry</div>
<div>Robert Stroud Laboratory</div>
<div><a moz-do-not-send="true" href="mailto:pascal@msg.ucsf.edu">pascal@msg.ucsf.edu</a></div>
</div>
</div>
</span><br class="Apple-interchange-newline">
</span><br class="Apple-interchange-newline">
</div>
<br>
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