VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 04 2007 - 15:31:53 CDT

Hi,
  VMD itself doesn't allow you to add/delete atoms interactively.
The way structure editing like this is typically done is by saving
a subset of the original structure to a new file and then loading
the new edited structure into a new molecule in VMD. This is
(in part at least) how the molefacture plugi does structure building,
for example. If you have identified the water molecules you want
to eliminate by selecting them and adding labels, you can then create
an atom selection that excludes these, and write a new structure file
that eliminates them. (e.g. File->Save Coordinates)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 04, 2007 at 03:21:33PM -0300, Atila Iamarino wrote:
> Dear all,
>
> I've tried to solve my problem looking in the mailing list but with no
> luck. How can I select visually and remove water molecules using VMD?
>
> Thank you,
>
> --
> Atila Iamarino
> L.E.M.B. - Laboratory of Molecular Evolution and Bioinformatics
> Av. Prof. Lineu Prestes, 1734 - USP (University of São Paulo) - ICB
> Zip: 05508-000 Phone: +55 11 30917290 / +55 11 30918453 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078