<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Samuel Flores <<a href="mailto:samuelfloresc@gmail.com">samuelfloresc@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">November 22, 2010 4:28:19 AM CST<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Wee Kiang Yeo <<a href="mailto:weekiang@gmail.com">weekiang@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: Queries regarding using RNABuilder for threading RNA-ligand complex</b><br></span></div><br><div>Absolutely! <br><br>for example, let's say the template is strand "A". Then:<br><br>constrainToGround A 15<br><br>fixes the position of the C3* atom of residue 15 of chain A to ground. If you have rigidified the entire template, you can choose any residue within it .. but it's better to choose one near the geometric center.<br><br>You might also find it useful to set the constraintTolerance parameter to something lower. By default, the above constraint is enforced within .005 in all its internal coordinates. <br><br>Where are you studying? I run RNABuilder workshops frequently, maybe you and your department would be interested in one at some point.<br><br>Sam<br><br><br><br>On Nov 22, 2010, at 3:20 AM, Wee Kiang Yeo wrote:<br><br><blockquote type="cite">Dear Dr Flores,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Two days ago, I have used RNABuilder to thread an RNA sequence through<br></blockquote><blockquote type="cite">a X-ray structure of 23S RNA (obtained from PDB). This X-ray structure<br></blockquote><blockquote type="cite">contains a ligand in a binding pocket. The original intention of<br></blockquote><blockquote type="cite">threading the RNA sequence was to ascertain the nucleotide residues<br></blockquote><blockquote type="cite">located near the ligand. However, during threading, the template X-ray<br></blockquote><blockquote type="cite">structure actually translocated in 3D space, leaving the<br></blockquote><blockquote type="cite">previously-bound ligand behind.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">My question: Is there a way to fix the position of the RNA-ligand<br></blockquote><blockquote type="cite">complex template during the threading process? If so, I would<br></blockquote><blockquote type="cite">appreciate it if you can give me an example of how to do so.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Regards,<br></blockquote><blockquote type="cite">Wee Kiang YEO (Mr)<br></blockquote><br></div></blockquote></div><br></body></html>