From: Giacomo Fiorin (
Date: Thu Dec 29 2022 - 14:24:54 CST

Hi Camps, can you define a sub-set of atoms (at least three) that the
molecules have in common and use that as the selection? If they don't
really have a common structure, you are probably out of luck for aligning
them rotationally, but at least you can center them all on the origin by
selecting them one at a time and do the following:

$sel moveby [vecscale -1.0 [measure center $sel]]

On Thu, Dec 29, 2022 at 3:06 PM 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