VMD-L Mailing List

From: J. Rui Rodrigues (jrui_at_ci.uc.pt)
Date: Fri Oct 08 2004 - 10:18:30 CDT

Hi,
You have computed rmsd values but you are not showing them. You can set a
variable to the rmsd value and then print that variable value.

set rmsd1 [measure rmsd $tempall2 $tempall1]
puts "$rmsd1"

You may also prefer to do this in one step:

puts "[measure rmsd $tempall2 $tempall1]"

Hope this helps,
Rui Rodrigues

vivek sharma <vivek.sharma_at_helsinki.fi> escreveu:

>
> 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,
>
> --
> VIVEK SHARMA
> HBG BI
>
> 

-- 
J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal