From: Josh Vermaas (
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
(, 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