Hi Claire,
All you need to do is:
1) Create selections for the two atoms you want to H-bond. There are
several different ways to do this in PyMOL (see the manual for details),
but for example, to bond
chain A, Thr 15 OG1
chain D, Asp 184 OD1
you would do
select donor, A/15/OG1
select acceptor, D/184/OD1
2) Create a h-bond object between these selections. The easiest way is
to use PyMOL's distance command which draws a dashed line between
them. It also shows the distance as a label, but you can turn this off
distance hbond, donor, acceptor
hide labels, x
3) Play with the settings to get it to look how you want. Dashed lines
sometimes look a bit odd when you ray-trace them - I find that
set dash_length, 0.15
set dash_radius, 0.09
set dash_width, 3.00
looks good. You can put these commands in your .pymolrc to save typing
them all the time.
Hope that helps,
Gareth
On Sun, 2003-11-09 at 09:58, Claire Sharpe wrote:
Hi there,
Sorry I'm going to ask probably a very basic question but could anyone
tell me how to create H-bonds in pymol?
I used SPDB viewer to model the interface between two dimers in a
tetrameric molecule. I now need to create some good pictures of this for
my thesis as SPDB isn't really good enough. I'd like to represent H-bonds
(not bond distances just bonds) e.g between ThrOG1 of subunit A and
Asp184OD1 of subunit D. I'm presuming that pymol can do this-if so would
really appreciate it if anyone could tell me how to enter in the command
line as I'm afraid I'm not used to it and thesis deadline looms on thurs!
Many thanks,
Claire
***
Claire Sharpe
Department of Biochemistry
University of Cambridge
80, Tennis Court Road
Cambridge. CB2 1GA
U.K
Tel: 01223 766045
Fax: 01223 766002
email: ce...@mole.bio.cam.ac.uk
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Gareth Stockwell gar...@ebi.ac.uk
European Bioinformatics Institute
