VMD-L Mailing List

From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Fri Nov 18 2005 - 03:42:29 CST

Hi,
thanks to all for the precious help. My problem is that I don't know tcl
.... (prefer python/perl)
Anyway, this below works fine but it does only the rmsd calculation for
the first pro_1.pdb with the rest of the files.

set outfile [open rmsd.dat w]
mol load pdb pro_1.pdb
set sel1 [atomselect 0 "protein and backbone"]
set lig1 [atomselect 0 "segid B"]
for { set j 2 } { $j < 100 } { incr j } {
    mol load pdb pro_$j.pdb
    set ID1 [expr $j-1]
    set sel2 [atomselect $ID1 "protein and backbone"]
    set lig2 [atomselect $ID1 "segid B"]
    set all [atomselect $ID1 all]
    $all move [measure fit $sel2 $sel1]
    set rmsd [measure rmsd $lig2 $lig1]
    puts "RMSD of 1 and $j is $rmsd"
    puts $outfile "RMSD of 1 and $j is $rmsd"
    puts Done
}

In fact, if I use another loop to compare pro_2.pdb with rest and so on,
vmd or tcl or whatsoever obscure to me does not go inside of the second
loop (Loop 2) and I don't know why:

set outfile [open rmsd.dat w]
# 1st Loop
for {set i 1} {$i < 100} {incr i} {
    mol load pdb pro_$i.pdb
    set ID [expr $i-1]
    set sel1 [atomselect $ID "protein and backbone"]
    set lig1 [atomselect $ID "segid B"]
# 2nd Loop
    for { set j 2 } { $j < 100 } { incr j } {
            mol load pdb pro_$j.pdb
        set ID1 [expr $j-1]
            set sel2 [atomselect $ID1 "protein and backbone"]
            set lig2 [atomselect $ID1 "segid B"]
            set all [atomselect $ID1 all]
            $all move [measure fit $sel2 $sel1]
            set rmsd [measure rmsd $lig2 $lig1]
            puts "RMSD of $i and $j is $rmsd"
            puts $outfile "RMSD of $i and $j is $rmsd"
            puts "Done"
        }
}

Then, Luis could you send me the procedure how to test your plugin?
Reading in your web page, it seem working only on trajectories, or am I
wrong?

Regards,

andrea 

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