From: Axel Kohlmeyer (
Date: Tue Feb 10 2015 - 22:34:17 CST

On Tue, Feb 10, 2015 at 10:51 PM, Majid Shahbabaei
<> wrote:
> 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?

you cannot. full stop. VMD is not a molecule editor and it will not
become one, no matter how much you explain and ask.

> I have read the mailing list to find some similar question but I could not
> find much things regarding to my problem.

you cannot find anything but what john already explained to you. there
is an alternate route avoiding the temporary file and using the
topotools plugin instead, but under the hood it uses the same method,
i.e. create an atom selection function for the atoms you want to keep
and then create a new VMD molecule from this selection and copy all
properties over. that's it.


> I would be greatly appreciated if you share your comments
> Thanks in advance
> MajiD
> 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

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.