From: Ashar Malik (
Date: Wed Jan 24 2018 - 08:02:02 CST

The atomselection language within VMD allows you to select by

Chain, Residue number, residue name, atom index, atom names and distance
cutoffs etc.

Your backbone selections will probably have carbon atoms with some numbers
appended to "C" so you should look at using regular expressions. See

Coming back to your actual selection question

set sel_atoms [atomselect top "index 39 to 61"] # This will select atoms at
position 40 and 62 [index is offset by 1 (i think!!) from PDB lists]

One thing to take care of is that if you use two list of atoms (to
calculate the superposition -- using "measure fit"), they have to be equal
and they will be compared in a one-2-one order so the order is important.

Hope this is what you were looking for. If not, write back.

On Thu, Jan 25, 2018 at 2:18 AM, Heather Carson <>

> I am trying to align two molecules but they have different numbers of
> atoms. The main backbone is identical but the have a different length
> hydrocarbon chain. I was wondering if it was possible to select a certain
> range of atoms and align those? I am trying to do it via the tk consol but
> I cant seem to select atoms number 40 to 62 (3 6 carbon rings which are
> connected) and align those in each molecule.