<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><font class="Apple-style-span" face="'Lucida Grande'"><div></div></font></div></div><div><br><div><div>On Jan 12, 2009, at 6:35 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Dave,<br>Me again - I forgot to mention that there is also a command to measure RMSD between sets of atoms without fitting them (it just uses their current positions):<br><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html</a>><br><br>You could fit on the three pairs of atoms using the "match" command, then use this "rmsd" command to measure RMSD between other sets of atoms without changing the fit. I wasn't sure from your mail whether that was something you wanted to do.<br>Best,<br>Elaine<br><br>On Jan 12, 2009, at 1:33 PM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Dave,<br></blockquote><blockquote type="cite">With the "match" command you can specify the exact atoms to fit, and<br></blockquote><blockquote type="cite">the resulting RMSD will be reported in the Reply Log. The main thing<br></blockquote><blockquote type="cite">to be careful about is specifying the atoms in the proper order. One<br></blockquote><blockquote type="cite">way is by name, another is to pick them in order from the graphics<br></blockquote><blockquote type="cite">window (Shift-Ctrl-click).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Specifics on how to use the "match" command:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">More general information on various matching methods:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I hope this helps,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Jan 12, 2009, at 1:32 PM, David Chenoweth wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Dear Chimera team,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Hi! I have two ligands in two different PDB files which have a very<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">similar core structure. I have constructed a framework of dummy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">atoms based on the centroids of several aromatic rings to use as a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">positioning system for the two ligands. I have three points/dummy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">atoms for each ligand in space in their respective pdb files and I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">would like to overlay or map the three points of one onto the three<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">points of the other so I can make measurements in chimera. Is there<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a simple way to open the two pdb files, select the three points that<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">belong to each ligand and overlay them (maybe even minimize the rms<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">deviation between them with some kind of fit to the plane defined by<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the three points). I can do this by hand and get them close but not<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">exact. I would also like to be able to calculate the rms deviation<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">between similar atoms in the core structure if possible.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks in advance,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dave Chenoweth<br></blockquote></blockquote><br></div></blockquote></div><br></div></body></html>