A more informative distance to measure between two aromatic (or planar) groups would be the plane-to-plane separation. I don't know how to code that, but if anyone out there has done, maybe it would make a handy addition to the set of tools.
Pierre Rizkallah ******************************************************************************* Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K. Phone: (+)44 1925 603808 Fax: (+)44 1925 603124 e-mail: p.j.rizkal...@dl.ac.uk html: http://www.srs.ac.uk/px/pjr/ -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell Sent: 24 May 2005 10:44 To: Grégori Gerebtzoff Cc: 'Sara Nichols'; pymol-users Subject: RE: [PyMOL] distance between aromatic residues On Tue, 2005-05-24 at 11:34 +0200, Grégori Gerebtzoff wrote: > 3) define two interlaced loops and calculate the distance between all > 6 carbons of Phe1 with all 6 carbons of Phe2, either with cmd.dist or > with simple mathematical functions; sum these distances > > 4) divide the result by 36, and export the data! Or more simply, once you have selected the 12 atoms, calculate the centroids of each of the two rings. Then just compute the distance between these centroids. This is a bit more efficient than doing 36 pairwise distances. Gareth ------------------------------------------------------- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_idt12&alloc_id344&opk _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
