<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Apr 25, 2008, at 7:32 AM, bala wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><font face="Arial" color="#000000" size="2"><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0pt; margin-left: 0in; line-height: normal; "><span style="FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: 'Arial','sans-serif'; mso-fareast-font-family: 'Times New Roman'">Dear chimera friends,</span><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0pt; margin-left: 0in; line-height: normal; "><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"> <o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0pt; margin-left: 0in; line-height: normal; "><span style="FONT-SIZE: 10pt; FONT-FAMILY: 'Arial','sans-serif'; mso-fareast-font-family: 'Times New Roman'">I have a simulated trajectory of a RNA molecule. I want to make a correlation plot based on residue fluctuation. I am new to scritping in python. Can anybody please give me some suggestions or any sample script for such analysis if possible.</span></div></font></div></blockquote><br></div><div>Hi Bala,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Is there any particular reason you want to do it in Chimera? It seems that Simulaid (<a href="http://atlas.physbio.mssm.edu/~mezei/simulaid/">http://atlas.physbio.mssm.edu/~mezei/simulaid/</a>) can do the plotting you're asking about, and it's free to academics.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If there is a particular reason you want to use Chimera, I can provide the programming details related to reading/processing a trajectory. In that case it would be helpful if you could say what format your RNA trajectory is in.<br></div><div><br></div><div>--Eric</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br class="Apple-interchange-newline"> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div></div><br><div></div></body></html>