VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 20 2006 - 15:31:28 CST

Hi,

> >When using 'measure hbonds', you should avoid having the same atom listed
> >in both the $selection1 and $selection2 parameters if you desire to have
> >reliable results, there's a warning about this in the manual as you've
> >already noted.
> in my case
> "name OW" gives the list of all oxygen atoms
> "index 5" is one of them
> so this violates the rule mentioned above :( however, i don't know how
> to ensure that the one oxygen of interest isn't contained. my intention
> would be probably (pseudo-code)

You can exlude things from an atom selection like this:
  set ow [atomselect top "name OW and not index 5"]

The "and not" does the job in this case.

See the docs on combining atom selection terms to include
and exclude multiple parts. The boolean operators are
quite useful for this sort of thing:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node76.html#4774

Try that out...

  John 

-- 
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