From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Mar 03 2014 - 16:27:05 CST

Hi Dawid,

Sure. Just write a script/use the RMSD trajectory tool. Since you are
dealing with 50 structures, and loading them by hand is a pain, I'd use
the Tcl scripting interface (it will save you alot of trouble later on).
The script would:

Load the reference structure
Make some atomselection that will be your reference (ref)
Make a loop over the 50 others{
Load the new structure
Make an atomselection that is the same size as the reference selection (sel)
Make an atomselection that includes the whole structure (all)
$all move [measure fit $sel $ref] ; #Does the movement.
Save the new coordinates to a new file
Cleanup (delete atomselections made inside the loop, possibly delete the
molecule too)
}
Be happy.

To implement this, you should familiarize yourself with the "mol" and
"atomselect" commands
(http://www.ks.uiuc.edu/Research/vmd/current/ug/node119.html), the exact
structure and contents of which will change depending on how you setup
the files/what features of the system are interesting to you.

Good luck!
-Josh Vermaas

On 03/03/2014 03:25 PM, Dawid das wrote:
> Dear vmd specialists,
>
> I want to do following thing.
> Let's say I have a reference structure and 50 others.
> Now I want to align those 50 on the reference structure.
> When I do it I want to save new xyz coordinates for 50
> transformed structures. Is it possible at all?
>
> How do I specify that my first structure is actually the reference one?
>
> Thanks in advance,
> Dawid Grabarek