VMD-L Mailing List

From: Jorge Pikunic (jorge.pikunic_at_bioch.ox.ac.uk)
Date: Fri Oct 08 2004 - 10:29:25 CDT

Hi,

if you want to print the rmsd's, maybe do something like:
                set rmsd1 [measure rmsd $tempall2 $tempall1]
                puts "before $rmsd1"
                $tempall2 move $tmat
                puts "$y with $x"
                set rmsd2 [measure rmsd $tempall2 $tempall1]
                puts "after $rmsd2"

Jorge

On Fri, 2004-10-08 at 15:01, vivek sharma wrote:
> Sir,
>
> please let me know why this loop does not work? I am trying to superpose
> various structures on each other and calculate rmsd before and after
> superposition, although it runs and prints the 'puts' text but doesnot print
> the rmsd values and transformation matrix in console.
>
>
>
> ----------
> #loop shown here, this is a part of program, before this code pdbs are #loaded.
>
> for {set y 0} {$y<4} {incr y} {
> for {set x [expr {$y+1}]} {$x<4} {incr x} {
> set tempall1 [atomselect $y "all"]
> set tempall2 [atomselect $x "all"]
> set tmat [measure fit $tempall2 $tempall1]
> measure rmsd $tempall2 $tempall1
> $tempall2 move $tmat
> puts "$y with $x"
> measure rmsd $tempall2 $tempall1
> }}
>
> I think there is some silly mistake, I am doing? Please clarify.
>
> Thanking you,
>
> sincerely,