From: Ajasja Ljubetič (
Date: Tue Jul 16 2013 - 10:57:40 CDT

Yes, but you have to do a bit of TCL scripting.
An understanding of atomselections and the "measure fit " command will be
useful. The are various TCL example scripts floating around the internet
that show how to loop through all frames of the trajectory.


On 16 July 2013 16:18, Andrei Tudor <> wrote:

> Hello,
> I am trying to center a system around the backbone of a protein, just like
> the align from RMSD Trajectory Tool does, but from command line.
> Is there such a command already implemented?
> Thanks,
> Andrei