VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Aug 23 2007 - 23:24:09 CDT

Hi,

On Thu, Aug 23, 2007 at 11:19:35PM -0400, Myunggi Yi wrote:
> I want to select two atom sets to superimpose two molecules.
> However, VMD always ignore my selection order.
>
> set sel [atomselect 1 "index 6 7 8 1 2 3 4"]
> set ref [atomselect 0 "index 1 2 3 5 6 7 8"]
> $sel get index
> returns 1 2 3 4 6 7 8

This is the expected behavior.

> Then how can I do the right rms fitting?

You can achieve this by passing an order parameter to 'measure fit'. The
order is a 0-based list that reorders the second selection. In your
case, you want something like (assuming I got the order right :-)):

measure fit $sel $ref order {3 4 5 6 0 1 2}

It seems though that this option to 'measure fit' is not docummented in
the user guide or the command usage yet.

Cheers,
Leo 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign