<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jan 16, 2008, at 8:19 AM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Monaco" size="4" style="font: 14.0px Monaco">I was unable to find how to get a plot of RMSD against time. I would like to do</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Monaco" size="4" style="font: 14.0px Monaco">that for the ligand (which is a single big residue) and selected residues of</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Monaco" size="4" style="font: 14.0px Monaco">the protein.</font></p> </blockquote><br></div><div>Mmmm, RSMD compared to what? Frame 1?</div><div><br class="webkit-block-placeholder"></div><div>You can't get such a plot right now, but what you can do is open your trajectory and also open a PDB file with whatever structure you want to measure RMSD with, and in the "Define script..." dialog put:</div><div><br class="webkit-block-placeholder"></div><div>echo <FRAME></div><div>match #0<+atom spec you wanted compared> #1<+atom spec you want compared></div><div><br class="webkit-block-placeholder"></div>Then if you play through the trajectory, in the reply log will be pairs of lines like this:<div><br class="webkit-block-placeholder"></div><div>23</div><div>1.264</div><div><br class="webkit-block-placeholder"></div><div>which is the frame number and the RMSD.</div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><br class="webkit-block-placeholder"></div></body></html>