From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 27 2007 - 14:57:12 CDT

Tom,
  Yes, I will add it to the documentation. This is something I added
short-term to solve problem that (at the time) only a few people were having,
and at the time I was (as always) completely overwhelmed with other development
activities and I never got around to adding docs for this feature.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 27, 2007 at 09:34:15AM -0500, Thomas C. Bishop wrote:
> 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
> >
> --
> ***********************
> * Thomas C. Bishop *
> *Office: 504-862-3370 *
> *CCS: 504-862-8391 *
> *Fax: 504-862-8392 *
> ***********************

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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