VMD-L Mailing List

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

Hi Camps,

I’ve had success with USAlign + some tcl scripting. https://urldefense.com/v3/__https://zhanggroup.org/US-align/__;!!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.

-Josh

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

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