VMD-L Mailing List

From: Eduardo Oliveira (eduardoftoliveira_at_gmail.com)
Date: Thu May 26 2011 - 05:56:40 CDT

Good morning
I've been trying to superimpose two pdb structures using the measure
fit command, but I keep having misaligned molecules.
The 3 atoms I choose to superimpose are exactly at the same distance
in both pdb's, so I should have a perfect alignment. I made 2 pdbs
with only the 3 atoms I want to allign so you can try to replicate my
problem (I want to superimpose pdb2 into pdb1).
I'm using vmd 1.8.7 and I type the following commands

vmd > set reference_sel [atomselect 0 "all"]
vmd > set comparison_sel [atomselect 1 "all"]
vmd > set move_sel [atomselect 1 all]
vmd > set transformation_matrix [measure fit $comparison_sel $reference_sel]
{0.6737986207008362 0.5753872394561768 -0.46359989047050476
-16.962047576904297} {-0.2173646241426468 0.7539900541305542
0.6198800206184387 27.565969467163086} {0.7062209248542786
-0.31690412759780884 0.6331063508987427 -12.475563049316406} {0.0 0.0
0.0 1.0}
vmd > $move_sel move $transformation_matrix

Thank you