VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Sep 15 2015 - 01:40:02 CDT

If you want to align the frames using only translations you can move by the difference of the centers of mass. Measure fit will always rotate.

Norman Geist

-----Ursprüngliche Nachricht-----
Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Simon Dürr
Gesendet: Montag, 14. September 2015 17:16
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: Align only translation not rotation

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