From: Axel Kohlmeyer (
Date: Thu May 19 2011 - 11:17:37 CDT

On Thu, 2011-05-19 at 16:43 +0100, ban arn wrote:
> Dear VMD users
> Is it possible to align two proteins of varying atom numbers according
> to backbone in vmd.


create selections, compute the required transformation matrix
with measure, if needed with a suitable "order" list. and then
apply to selection with all atoms. its been discussed on the
list several times. just search the archives for details and
find the remaining information in the user's guide.


> Kindly advice
> Many Thanks
> Balaji

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.