From: Vermaas, Josh (
Date: Fri Dec 30 2022 - 11:00:34 CST

Hi Camps,

I’ve had success with USAlign + some tcl scripting.;!!DZ3fjg!_d37hhVOFFquMezJzmuuApMEvuqLXYa-XYJp5L0stm76U6gWtGCq8eIU6yMm_lYHXq3K2ww7wtm3v-MQ5D0$
In my case, I was interested in aligning some alphafold structures that multiseq didn’t recognize as being similar enough. The procedure I used is below, which would align structures in prot_X.pdb with the structure in prot_1.pdb.

proc align { dirname i } {

        exec ./USalign $dirname/prot_$i.pdb $dirname/prot_1.pdb -o $dirname/prot_$i


At some point, I’d really like to include USAlign into VMD proper somehow, since its super flexible, but I haven’t had a chance to do this properly.


From: <> on behalf of "I. Camps" <>
Date: Thursday, December 29, 2022 at 3:25 PM
To: "" <>
Subject: vmd-l: << Centering/aligning several molecules >>


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.