From: John Stone (
Date: Thu Dec 29 2022 - 13:54:56 CST

  You might try using the MultiSeq plugin's multiple structure-multiple sequence
alignment (via STAMP) to do this (In Extensions | Analysis | MultiSeq).
Within MultiSeq, you can use the Tools | Stamp Structural Alignment
menu to align all, or specific molecules, chains, subsequences, etc.

  John Stone

On Thu, Dec 29, 2022 at 04:26:04PM -0300, I. Camps wrote:
> Hello,
> I loaded 5 molecules in VMD. They have different sizes/number of atoms and
> their origins are in different positions.
> Now, I want to center (superimpose) all the molecules.
> Using align or measure fit is not possible because the number of atoms is
> different between them.
> Any help is welcome.
> Regards,
> Camps

Research Affiliate, NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801