VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Aug 18 2016 - 14:54:16 CDT

Hi all,

this is probably a simple thing, but I can't figure out how to write a
selection correctly. I would like to print out indices for all CA
atoms in certain chains in my pdb file. Here is a selection that I
make:

set sel [atomselect top "chain A B C and name CA]
$sel list

(or $sel get index)

Then when printed all indices are shifted by 1 from the number it
supposed to be. The line in the pdb file looks like this:

ATOM 5 CA THR A 1 60.252 86.999 118.788 0.00 0.00 A
..
..
ATOM 19 CA SER A 2 62.852 89.569 117.619 0.00 0.00 A

and so on, but the numbers I get printed out in the tcl shell are like this:

4 18 ... etc.

So when I call list or index the atoms are numbered starting from 0.

Is there a way to make atomselect print the actual index (in my case.
5, 19... and so on) ?

Thanks in advance!

Olga