VMD-L Mailing List

From: Camilo Andrés Jimenez Cruz (camilo.jimenezc_at_gmail.com)
Date: Fri Dec 13 2013 - 09:35:37 CST

Hi everybody.

I have been fighting with this for a while now, so I decided to scream for
help...

I have a ligand (segname P3) in a pocket (segname P1), and want to draw the
hydrogen bonds between them. To do this I tried selecting the Os from one
and the Ns from the other and then backwards (This is an all atom
structure, so it includes Hs). One of such selections would read

(segname P1 and name "O.*" and within 4 of segname P3) or (segname P3 and
name "N.*" and within 4 of segname P1)

if I use CPK representation, the selected atoms look right. Now, If I use
HBonds representation (4 Amstrongs, 40 degrees), it draws some good ones,
but it also draws some between Os in P1 and random Hs around.

I looked all over the mailing list (well, not all over, but did quite some
googling around) and the closest thing that I found mentioned was Axel K.
suggesting to write a script to alleviate this. (
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3841.html).

Any suggestions? ideas of what am I doing wrong? do I need to write a TCL
script and draw CG objects instead?

Thanks in advance

-- Camilo Jiménez