From: Majid Shahbabaei (
Date: Tue Feb 10 2015 - 21:51:56 CST

Dear John, Tim, Michail and Users,

Thank you very much for your helps. Sorry for my poor explanations in the
previous email. Let me be more precise in details. I am trying to build a
model composed of a carbon box combined to a pore element. I need to make
two holes in the left and right sides of the box before combining the pore
element. I could specify that of which atoms should be removed. So, my
question is that by knowing the atom ID how can I delete some atoms?
I have read the mailing list to find some similar question but I could not
find much things regarding to my problem.

I would be greatly appreciated if you share your comments

Thanks in advance


On Wed, Feb 11, 2015 at 12:59 AM, John Stone <> wrote:

> Hi,
> 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
> Cheers,
> 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