From: andrea spitaleri (
Date: Fri Nov 18 2005 - 10:16:01 CST

Hi again :),
thanks for your suggestion. However, I worked out doing that (thanks to
Luc) much faster:

set outfile [open rmsd.dat w]
for { set k 1 } { $k < 101 } { incr k } {
    mol load pdb pro_$k.pdb
set mol_list [molinfo list]
foreach mol $mol_list {
    set sel1 [atomselect $mol "protein and backbone"]
    set lig1 [atomselect $mol "segid B"]
    foreach mol1 $mol_list {
        set sel2 [atomselect $mol1 "protein and backbone"]
        set lig2 [atomselect $mol1 "segid B"]
        set all [atomselect $mol1 "all"]
        $all move [measure fit $sel2 $sel1]
        set rmsd [measure rmsd $lig2 $lig1]
        puts $outfile "$mol $mol1 $rmsd"
        puts "DONE"
close $outfile



Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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