Sergio, We use the term "polar contacts" because, as you correctly point out, some of the contacts shown don't meet strict hydrogen-bonding criteria. Of course, many macromolecular crystal structures aren't of high enough resolution to make definitive determinations anyway...so...
With ideal geometry, PyMOL will show polar contacts out to: set h_bond_cutoff_center, 3.6 With minimally acceptable geometry, PyMOL will show polar contacts out to set h_bond_cutoff_edge, 3.2 These settings can be changed *before* running the detection process (dist command mode=2 or via the menus). Note that the hydrogen bond geometric criteria used in PyMOL was designed to emulate that used by DSSP. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Sergio E. Wong > Sent: Monday, May 23, 2005 7:13 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] polar contact definition > > Dear Pymol users: > > I'm using pymol to find "polar contacts". I'm wondering > what is the > definition of a "polar contact". Some of the distances are > longer than > expected for a hydrogen bond. So, I'm left wondering what is > the distance cut off employed. > > Thanks > > -Sergio > > > ------------------------------------------------------- > 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_id=7412&alloc_id=16344&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
