VMD-L Mailing List

From: ziemys_at_ecr6.ohio-state.edu
Date: Mon May 08 2006 - 09:50:55 CDT

Hi,

I want to calculate RMSD of subset AFTER I "fit" and "move" ? Say, I fit the protein in each frame and move the whole system :

$p_mov frame $i
$p_ref frame [expr $i - 1]
$sys_m frame $i
$sys_r frame [expr $i - 1]
$sys_m move [measure fit $p_mov $p_ref]

Will I get the new coordinate values for RMSD calculation of subset in system, if i will try something like:

set x [atomselect top "index 1" frame $i]
set y [atomselect top "index 1" frame [expr $i - 1]]
puts "[measure rmsd $x $y]"

If not, then how to access the coordinates of moved selections ?

Arturas