<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Elisabeth,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Also, naturally there is also a Python interface to findclash if that's what you're looking for. It's in DetectClash/__init__, either the detectClash() function or the cmdDetectClash() function depending on your needs.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 16px; "><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><br class="Apple-interchange-newline"></div><div><div>On Feb 28, 2011, at 9:21 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote:<br><blockquote type="cite"><br></blockquote><blockquote type="cite">I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? <br></blockquote><blockquote type="cite"><br></blockquote>Hi Elisabeth,<br>With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes. The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active. With the command, it would be something like<br><br>findclash #1 test #2 [other options]<br><br>Another example:<br>findclash ligand overlap -0.4 hb 0 test aromatic<br><br>Use command "help findclash" to see the manual page, or view it here:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html</a>><br><br>With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply. Click the Help button to see the manual page, or view it here:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html</a>><br><br>This is more of a <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list.<br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div><br><br></body></html>