<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sharon,<div><span class="Apple-tab-span" style="white-space:pre"> </span>It seems to me that there are some issues with this. In particular you need the helices you are measuring to maintain their helicity throughout the trajectory otherwise you will get meaningless angle values for frames with poor helicity (the computed axis direction will be fairly random). Also, to identify the helixes there have to be specific residues that always participate in the helix -- which I imagine would usually be the case but I can envision scenarios where a helix winds/unwinds up and down a sequence.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Within those constraints, you can measure an inter-helical angle with the Python script I've attached. You would use it in MD Movie's Per-Frame->Define Script dialog (choose "Python" in "Interpret script as"). You would need to change the specific residue numbers in the script to correspond to the "core" (non-unraveling) resides of your helices. The angles will be printed to the Reply Log as the trajectory plays.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Let me know if you have any questions/problems.</div><div><br></div><div>--Eric<br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Apr 14, 2009, at 10:38 AM, Shuanghong Huo wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div><font face="Arial, sans-serif" size="2"><div>Dear Chimera Developers,</div><div><font face="Times New Roman, serif" size="3"> </font></div><div>My group needs to calculate the inter-helical angle for a large trajectory. We know Chimera can calculate the inter-helical angle for a conformation. We are wondering what the easiest way to use Chimera to process the whole trajectory. It is amber trajectory.</div><div><font face="Times New Roman, serif" size="3"> </font></div><div>Thanks,</div><div>Sharon Huo, Ph.D.</div><div>Associate Prof. of Chemistry & Biochemistry</div><div>Clark University</div></font></div></span></blockquote><br></div><div><br></div><div><br></div></div></body></html>