<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi Ian,<div><div><div><div>Dock Prep now rebuilds truncated sidechains using data from rotamer libraries (Dunbrack or Richardson):</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html</a></font></div></div><div><br></div><div>It automatically locates the truncated sidechains, retrieves rotamer information, and chooses the best rotamer based on clashes, H-bonds, and (by default) backbone conformation. This may take a while... it sounds like your system is pretty large. It will not add in missing backbone segments or entire residues, however, only sidechains. </div><div><br></div><div>Dock Prep was changed after the last production release (Nov 2007), so I recommend getting a daily build:</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/chimera/alpha-downloads.html">http://www.cgl.ucsf.edu/chimera/alpha-downloads.html</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div></div><div>Best,</div><div>Elaine</div><div>-----</div><div><div>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a></div><div>UCSF Computer Graphics Lab and Babbitt Lab</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a></div><div><br class="khtml-block-placeholder"></div><div>On May 1, 2008, at 10:08 PM, Ian Yarbrough wrote:</div></div><div><div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br>A model that I am working with has several missing or partial side chains, and I'm dealing with about 80 subunits of this protein (organized into 3 chains). I am trying to repair these, but don't want to go through the task of finding every broken chain. Is there a way to get chimera to locate the broken ones and repair them all? I've seen the dock prep feature, but don't want to change them all to alanines. <br>Thanks for you help.<br><br>Ian Yarbrough<br>Texas A&M University<br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div></blockquote></div></div></div></div></div></body></html>