RE: [PyMOL] polar contact definition

[Warren D. <wa...@de...>]

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:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Sergio E. Wong
> Sent: Monday, May 23, 2005 7:13 PM
> To: pym...@li...
> 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
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>