VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 19 2004 - 10:11:32 CDT

Hi,
  Atoms can also be moved with atom selections:

  set sel [atomselect top "all"]

Built-in:
   $sel moveby {1 -1 3.4}

Or your own routines:
  proc mymoveby {sel offset} {
    foreach coord [$sel get {x y z}] {
      lappend newcoords [vecadd $coord $offset]
    }
    $sel set {x y z} $newcoords
  }
  mymoveby $sel {0.1 -2.8 9}

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 19, 2004 at 10:44:44AM +0200, Olaf Lenz wrote:
> Hello!
>
> Albert Sun wrote:
> > How to pick atoms, and remove them or change the position of the
> > selected atoms?
>
> You can move an atom/residue/etc. via
>
> VMD Main Menu->Mouse->Move->Atom (hotkey '5')
>
> You can't really remove an atom, as this would change the molecule's
> structure, and the structure is fixed (is that right?). What you can do,
> however, is to make an atom invisible. For that you simply need to select
> all the other atoms, for example:
> 1. press '0' and click on the atom. You'll get something like:
>
> Info) picked atom:
> Info) ------------
> Info) molecule id: 0
> Info) name: C4
> Info) type: C4
> Info) index: 279
> Info) resname: A
> Info) resid: 14
> Info) chain: B
> Info) segname:
> Info) x: 25.724001
> Info) y: 9.819000
> Info) z: 28.396000
>
> 2. select all atoms that are not the picked atom:
>
> not id 279
>
> Olaf 

-- 
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