From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Feb 12 2007 - 11:58:12 CST

No, it doesn't, and I am not sure if such a problem is well-defined
even. Your best bet would be to make selections of a certain subset
of relevant atoms of the same number and then align based on those.

On Feb 12, 2007, at 11:53 AM, namd vmd wrote:

> Does VMD allow structural alignment of two proteins with different
> number of residues ?