VMD-L Mailing List

From: Camilo Andrés Jimenez Cruz (camilo.jimenezc_at_gmail.com)
Date: Fri Dec 13 2013 - 13:20:07 CST

Reading the C++ source code that draws the representation I understand now
what's going on.

// This draws a hydrogen bond from atom 'i' to the hydrogen of atom 'k',
only
// if both are selected and meet the hbond distance and/or angle criteria
// distance is measured from heavy atom to heavy atom
// the angle is from heavy atom to hydrogen to heavy atom
// coloring is by the donor atom color specification

I think this could be added to the documentation (I didn't find it clear
from there)

-- Camilo Jiménez

On Fri, Dec 13, 2013 at 10:35 AM, Camilo Andrés Jimenez Cruz <
camilo.jimenezc_at_gmail.com> wrote:

> 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
>