VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu May 26 2011 - 07:43:12 CDT

Hi Eduardo,

In principle it is easy to align groups of 3 atoms, but some commonly
used algorithms only work well for 4 atoms or more. I think VMD's
algorithm has this limitation, the (rare) case of 3 atoms is
sacrificed in favor of fast and robust alignments for large
structures.

Cheers,
Jerome

On 26 May 2011 12:56, Eduardo Oliveira <eduardoftoliveira_at_gmail.com> wrote:
> 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
>