VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 26 2011 - 13:17:43 CDT

On Thu, May 26, 2011 at 8:43 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> 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

it is even better! VMD uses a different algorithm when 1 (simple translation),
2-3 (analytical transformation), or 4 and more atoms (use algorithm from:
Kabsch, Acta Cryst. (1978) A34, 827-828) are in the selection.
there are still some pathological cases with more than 4 atoms
where the latter algorithm can fail, but those are extremely rare.

cheers,
     axel.

> 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
>>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.