VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
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.
http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node79.html

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

http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node137.html#SECTION001050000000000000000
####

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 <hcarson1_at_sheffield.ac.uk>
wrote:

> 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.
> 

-- 
Best,
/A