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