<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"><base href="x-msg://2/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Josh,<div><br></div><div> I think the way to go is find an existing PDB DNA model and simply align it to your RNA by say matching the P backbone atoms. For example if the RNA is chain A of model #1 and the double stranded DNA is model #2 with chains A and B use a command like</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>match #2:3-15.A@P #1:1-13.A@P</div><div><br></div><div>I would not recommend using the Chimera RNA command which only builds very crude models with center-liine paths specified. <br><div><br></div><div> <a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html</a></div><div><br></div><div> Tom</div><div><br></div><div><br></div><div><div><div>On Sep 23, 2013, at 12:09 AM, Joshua Carter wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div class="hmmessage" style="font-size: 12pt; font-family: Calibri; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div dir="ltr">Hi,<div><br></div><div>I'm working on a project in chimera that involves modeling the binding of a RNA-guided protein complex to a double stranded piece of DNA. What I need to do is be able to is either match a DNA pdb to the existing RNA pdb I have or build one using the rna command in chimera. I know there is a path command, is there any way I could specify that to build along a pdb I have already? Or am I just barking up the wrong tree entirely?</div><div><br></div><div>Thanks,</div><div>Josh</div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div></body></html>