VMD-L Mailing List

From: Simon Dürr (simon.duerr_at_uni-konstanz.de)
Date: Mon Sep 14 2015 - 10:16:08 CDT

I'm using the following command to align one of the frames of my
simulation to frame 0 to better understand what the ILS tools
(ILS:shift_to_center) do.

I however run into a strange problem.

I do this:
set sel [atomselect top "protein and name CA"]
set molid [$sel molid]
set refid $molid
set ref [atomselect $refid [$sel text] frame 0]
set all [atomselect $molid all]

$sel frame 1
$all frame 1
set mat [measure fit $sel $ref]
set shift [lindex $mat 0 3]
lappend shift [lindex $mat 1 3]
lappend shift [lindex $mat 2 3]
$all moveby $shift

The command should carry out only the transformation part of the
alignment and omit the rotation. I therefore expect to see frame1
aligned on the frame0 with little differences due to rotation (the
frames are 1ns apart)
What I get instead is the protein aligned in the y-axis and frame X is
shifted on the x-z-plane about 5A away from the frame0.

Has anyone an idea why this happens?

Cheers,
Simon