Re: [PyMOL] list of hydrogen bonds

[Robert C. <rob...@qu...>]

Hi Martin,

On Wed, 11 Aug 2010 12:02:32 +0200 Martin Hediger <ma...@bl...> wrote:

> I was thinking about this as well, I saw an older post on this topic
> http://www.mail-archive.com/pym...@li.../msg06211.html
> but it seems that the script mentioned there starts to see 'hydrogen 
> bonds' between non-polar hydrogens and atoms up to 15 angstrom away.
> Can someone confirm on this?

I am the author of that script and I can confirm that there is a problem. :(
The script in that message has the cutoff distance and angle hardwired in at
3.7A and 55 degrees, respectively, and in theory it also selects only H-bonds
between "N" and "O" atoms, but there was a mistake in the code that used the
atom "ID" property rather than the "index" property.  Surprisingly (to me)
that makes a difference.

I have two newer scripts that from my testing work properly.  One will list
any H-bonds between two selections (list_hbonds.py) and the other is designed
to only list (and draw) all main-chain H-bonds (list_mc_hbonds.py). Both
scripts allow you to override the default cutoff values. You can get them from
my website:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

I have removed the old script from there as well.

Sorry about that!

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc