From: Víctor (victor.gil.sepulveda_at_gmail.com)
Date: Thu Jul 19 2012 - 07:41:45 CDT

Thanks a lot!

On Thu, Jul 19, 2012 at 2:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Jul 19, 2012 at 2:17 PM, Víctor <victor.gil.sepulveda_at_gmail.com>
> wrote:
> > I mean the superposition algorithm for rmsd calculation. In a script the
> > command would be measure fit if i'm not wrong.
>
> ok. from the sources:
>
> // find the best fit alignment to take the first structure into the second
> // Put the result in the matrix 'mat'
> // This algorithm comes from Kabsch, Acta Cryst. (1978) A34, 827-828.
>
> please note, that for up to three atoms in the selection,
> different approaches are used.
>
> HTH,
> axel.
>
> >
> > On Thu, Jul 19, 2012 at 1:55 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Thu, Jul 19, 2012 at 12:06 PM, Víctor <
> victor.gil.sepulveda_at_gmail.com>
> >> wrote:
> >> > Dear All,
> >> >
> >> > I've been playing around with a C++ implementation of a superposition
> >> > algorithm. When I've compared the results with VMD, I've noticed that
> >> > those
> >> > are different, but equal to other implementations of the same
> algorithm
> >> > I'm
> >> > using, so my code is correct.
> >> >
> >> > Does anybody know which superposition algorithm is VMD using?
> >>
> >> can you be a bit more specific about what "superposition"
> >> you are talking about. i.e. which commands exactly you
> >> are running in VMD.
> >>
> >> thanks,
> >> axel.
> >>
> >> >
> >> > Thanks!
> >> >
> >> > --
> >> >
> >> > Víctor Gil Sepúlveda
> >> > E. Informatica - FIB - UPC
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> >
> > --
> >
> > Víctor Gil Sepúlveda
> > E. Informatica - FIB - UPC
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>

-- 
Víctor Gil Sepúlveda
E. Informatica - FIB - UPC