From: ban arn (ban.arn_at_gmail.com)
Date: Fri May 20 2011 - 06:37:47 CDT

Dear VMD user

Kindly help me how to get new co-ordinate values for transforming matrix for
aligning two proteins of different atom numbers.

Say for example like this..

set transformation_matrix [measure fit $sel1 $sel2]
Info) {0.971188 0.00716391 0.238206 -13.2877}
{0.0188176 0.994122 -0.106619 3.25415} {-0.23757 0.108029 0.965345 -2.97617}
{0.0 0.0 0.0 1.0}

Balaji

On Fri, May 20, 2011 at 11:47 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, May 20, 2011 at 5:23 AM, ban arn <ban.arn_at_gmail.com> wrote:
> > Dear VMD users
> >
> > Thanks for reply.
> >
> > I tried to align two protein trajectories of varying atom numbers using
> > transformation matrix, its shows error as " the selection should have
> same
> > atom numbers"
> >
> > For example, I defined my selection as
> >
> > set sel1 [atomselect 0 "backbone"]
> > set sel2 [atomselect 2 "backbone"]
> > set transformation_matrix [measure fit $sel1 $sel2]
> >
> > "Measure fit" commands requires that the selection should have same atom
> > number.
> >
> > Kindly advice.
>
> kindly _follow_ the advice that has been given to you.
>
> search the mailing list archives for how to handle this.
>
> axel.
>
>
>
> >
> > Many Thanks
> > Balaji
> >
> >
> >
> >
> >
> >
> >
> > On Thu, May 19, 2011 at 6:07 PM, Eduard Schreiner
> > <eduard.schreiner_at_gmail.com> wrote:
> >>
> >> Axel's reply would work for that one too
> >> eddi
> >>
> >> On Thu, May 19, 2011 at 6:37 PM, ban arn <ban.arn_at_gmail.com> wrote:
> >>>
> >>> Dear VMD users
> >>>
> >>> Thnaks for reply.
> >>>
> >>> It works fine.
> >>>
> >>> I can pose the question in another way.
> >>>
> >>> Is it possible to align the trajectories of two proteins of varying
> atom
> >>> numbers according to backbone in VMD.
> >>>
> >>> Many Thanks
> >>> Balaji
> >>>
> >>> On Thu, May 19, 2011 at 5:31 PM, Joseph Bylund <
> joseph.bylund_at_gmail.com>
> >>> wrote:
> >>>>
> >>>> The stamp structural alignment in extensions->analysis->multiseq
> sounds
> >>>> like what you're looking for.
> >>>>
> >>>> On 05/19/2011 11:43 AM, ban arn wrote:
> >>>>>
> >>>>> Dear VMD users
> >>>>>
> >>>>> Is it possible to align two proteins of varying atom numbers
> according
> >>>>> to backbone in vmd.
> >>>>>
> >>>>> Kindly advice
> >>>>>
> >>>>> Many Thanks
> >>>>> Balaji
> >>>>>
> >>>
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>