VMD-L Mailing List

From: politr_at_huji.ac.il
Date: Sun Feb 22 2009 - 10:52:01 CST

Thank you for the suggestion but it doesn't work. May it be because I'm
using the short peptide of 16 residues? When I say it doesn't work I
mean that I'm getting some very strange presentation where I can't
understand what happened to the molecule
Regina

Axel Kohlmeyer wrote:
> On Sat, 21 Feb 2009, politr_at_huji.ac.il wrote:
>
> RP> Dear VMD users and developers,
>
> dear regina,
>
> RP> I would like to create a nice picture of peptide surrounded by water and I
> RP> want the peptide to be presented by surface and maybe water too. Does anyone
> RP> knows how to do it or maybe you can suggest some other nice way of
> RP> presentation. I just don't want it to be presented in sticks and balls etc.
>
> you could use SURF or MSMS to generate surfaces directly.
> a second option would be to use the volmap tool to generate
> a density map for a selection of atoms and then represent
> that with an isosurface representation. the density maps can
> be weighted by different atom parameters (mass, covalent radius,
> unweighted) and there are other flags to play with, so there
> are lots of options.
>
> it is difficult to make a specific suggestions, since your
> description of what you want to achieve is rather vague.
>
> cheers,
> axel.
>
> RP> Regina
> RP>
>
>