VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 24 2004 - 10:51:02 CDT

Hi,
  There are several differences in the way the HBonds representation
selects HBonds for rendering from the way they'd be selected by
Ahmet's script:
  1) The HBonds rep ignores any atoms that _already_ have bonds defined
     by structure file (PSF). Any atoms that are already "bonded" are
     ignored by the HBonds rep, and no bond will be drawn by this rep.
     (the bond _would_ be drawn by a lines or bonds rep however...)
 
  2) The HBonds rep only searches atoms that are among the list of
     selected atoms, if one of the two atoms in the HBond isn't
     selected, then the bond will not be drawn.

  3) The candidate bonds have to meet both the distance cutoff and
     angle cutoff criteria. If the angle cutoff isn't met, then the
     bond isn't drawn, even if it's within the correct distance, and
     vice-versa. (well, this should be the same as Ahmet's script actually)

  4) The HBonds rep only considers bonds with atoms that are regognized
     as hydrogens by virtue of their name beginning with "H", or in the
     form "xH" where 'x' is a digit. If this isn't true, then the atom
     is ignored.

I hope that helps clarify what is going on there.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 23, 2004 at 02:53:51PM -0400, Uday Chippada wrote:
> Hey all,
>
> I have a wierd problem with Graphical representation of hydrogen bonds. When I select drawing method as HBonds, and give a Distance cut off of 2.6, only hydrogen bonds with a length of less than 1.7 A are shown in the Display window. If I increase the cut off to 3 then only hydrogen bonds with length less than 2.3 -2.4 A are shown on the display window. I have used the TCL script (hbond.tcl) that Ahmet has so generously provided on the list a few days ago, to calculate the number of hydrogen bonds, and found that the script returns a lot more hydrogen bonds than what is being shown on the display screen.
>
> It would be great if anyone has any comments or can tell me what exactly is being represented on the display window.
>
> Thanx in advance
> Uday. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078