From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Tue May 31 2005 - 10:50:32 CDT

Hi Dmitry,

The RMSD Calculator (Extensions menu) has an alignment button. You may also
be interested in the Multiple Alignment tool. Some of the commands in this
script may be of interest:

proc align_frames {mol_id selection_text mol_id_to_align_to
{frame_to_align_to 0}} {
        set nf [molinfo $mol_id get numframes]
        puts "number of frames to align: $nf"
        set sel0 [atomselect $mol_id_to_align_to $selection_text frame
$frame_to_align_to]
        
        # align all molecules to one frame, beginning at frame 0
        for {set i 0} {$i<=[expr {$nf-1}]} {incr i} {
                set sel [atomselect $mol_id $selection_text frame $i]
                set sel_all [atomselect $mol_id "all" frame $i]
                $sel_all move [measure fit $sel $sel0]
                $sel delete
                $sel_all delete
        }
        $sel0 delete
}

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Dmitry Osolodkin
Sent: May 31, 2005 9:58 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Any way for comparing two structures??

Hi all,
I have a great interest in comparing two structures of one protein. I want
to
superimpose them and visualise results. Is there an automatic way in VMD to
do this (for example, like in NOC) or I need to superimpose them only
manually??

Dmitry Osolodkin