VMD-L Mailing List

From: Joseph Bylund (joseph.bylund_at_gmail.com)
Date: Thu Oct 20 2011 - 20:13:59 CDT

What about 3 representations:
1) segname A
2) segname B
3) ((segname A) and within 2 of (segname B)) or ((segname B) and within
2 of (segname A))

where segname A and segname B are however you want to select your two
sets of atoms, a bunch of atoms are in both, but the bonds are
exclusively in one set, you might have to vary the distance cutoff slightly.
-Joe

On 10/20/2011 08:07 PM, lam nguyen wrote:
> Hi all,
>
> In the graphical representation I use lines as the drawing method. In
> my system I name different segments (segname) as EVE, ODD and NEW. I
> want to use different colors for these categories so I can tell which
> bond (appearing as a line) belongs to which segment category. I also
> have bonds between atoms of different segments and want to color them
> differently from bonds on the same segments.
>
> For example, I have two segments of segname NEW. One has atoms A1,
> A2,... and the other has B1, B2, ... I color bonds between A's and
> bonds between B's as blue. And I want bonds between A's and B's as
> red. If there are few segments of segname NEW I can just create one
> representation for the whole system as red, then overlap it by a set
> of representations in blue - one for each segment. However there are
> quite many of such segments. If I use only one representation for all
> segments of segname NEW, the bonds between A's and B's will appear as
> blue. Is there any method I can use without creating lots of
> representations?
>
> Thanks,
> Lam