<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Feb 27, 2008, at 11:08 PM, bala wrote:</div><blockquote type="cite"> <!-- Converted from text/plain format --><p><font size="2">Dear chimera users,<br> <br> i) Greetings. I have a trajectory of 1000 conformations of a RNA molecule. I want to see the distribution of interphosphate distance. say i want to see the P-P distance of the residue 3 paired with a residue 38 in the opposite strand. Is it possible in anyways.<br> <br> ii) Suppose when i source a file from command line option : source dist, chimera nicely takes the distance commands in the file and displays the distances in the GUI. Is it possible to send the output to a file rather than seeing in GUI.<br></font></p></blockquote></div>The script that 吴超 was nice enough to forward will print out distances. If <i>not</i> run in nogui mode (i.e. normally, with the graphical interface) the distances will go to the Reply Log, and you can save them to a file from there. Furthermore, you can use the Per-Frame->Define Script menu item of MD Movie to have the script executed each frame. You may or may not want to prefix the output with the frame number; if you do you need to put mdInfo['frame'] somewhere in the print statement.<div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><br></div><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; "> 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></div></body></html>