VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Mon Aug 27 2007 - 09:34:15 CDT

Thanks! that's a very useful bit of information!!!

Please have someone insert this into the VMD documentation.

TOm

On Thu, 2007-08-23 at 23:24 -0500, Leonardo Trabuco wrote:
> 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
> 

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