From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Tue May 31 2005 - 14:07:45 CDT

Hi, you could also use the rmsdtt plugin to avoid the scripting:
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html

Best,

Luis

Blake Charlebois said the following on 05/31/05 11:50:
> 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