From: Norman Geist (
Date: Thu Nov 24 2016 - 01:39:44 CST

Hey, if you can break down the superimposable part of both proteins using
the same selection e.g. "backbone and name CA" you can easily use the RMSD
Trajectory Tool (Extensions->Analysis). If you need different selections for
both proteins, you can still do it at the commandline with TCL (untested):


set sel1 [atomselect 0 "resid 1 to 10 and name CA"]

set sel2 [atomselect 1 "resid 4 to 13 and name CA"]

set mat [measure fit $sel1 $sel2]

$sel2 move $mat;


If you need this for a number of frames I can give you an example of a loop
across all frames.


Norman Geist


Von: [] Im Auftrag von
Wong Li Zhe
Gesendet: Donnerstag, 24. November 2016 06:38
Betreff: vmd-l: Superimpose Models
Wichtigkeit: Hoch


Dear VMD users,


I would like to combine superimpose 2 protein models with different atoms

I wonder is there a way in which how I can alter the PDB file to achieve the
same atom numbers?

I have tried several approaches using Tk console and etc but it wont.

Any insight on this issue?


Thank you.


Best regards,

Li Zhe

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