From: John Stone (
Date: Tue Feb 10 2015 - 09:59:49 CST

  The easiest method is by making an atom selection that
excludes the atoms you want to delete, then write a new
structure file, and load the newly created structure file
into a new molecule:
  set sel [atomselect top "not someatomsyoudontwant"]
  $sel writejs temp.js
  $sel delete
  mol new temp.js waitfor all

  John Stone

On Tue, Feb 10, 2015 at 08:28:31PM +0900, Majid Shahbabaei wrote:
> Dear VMD-Users,
> I wonder to know that how can I delete some atoms with VMD command line?
> I would be greatly appreciated if anybody guides me?
> Thanks in advance
> MajiD

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349