<br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Try "Loopy". You can get it to build termini in addition to loops.<br>
<br>
<a href="http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy" target="_blank">http://wiki.c2b2.columbia.edu/<u></u>honiglab_public/index.php/<u></u>Software:Loopy</a><br>
<br></blockquote><div><br></div><div>I've also seen people use PyMOL's builder to do this. Either way, you'll need to take (a lot of) extra care to minimize your linker and make sure that it looks reasonable.</div>
<div><br></div><div>-Michael</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Nevertheless, I'd suggest simply omitting that part of the protein and capping your new terminus to remove the charge. You will have more difficulties converging the conformation of the unstructured terminus than you may expect. </blockquote>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
CHris.<br>
<br>
-- original message --<br>
<br>
Hi all,<br>
<br>
Is there a program that allows the user to add residues to the N and C<br>
terminus, without using the electron density? I would like to add a<br>
short linker to my protein which doesn't exist in the electron<br>
density.<br>
<br>
Thanks a lot,<br>
<br>
Sincerely,<br>
Zack<br><font color="#888888">
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Michael Lerner, Ph.D.<br>IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>Rockville, MD 20852 (UPS/FedEx/Reality)<br>
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