VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 26 2006 - 23:58:57 CST

Hi,
  Sorry for the delayed reply on this stuff, I was on vacation most of
last week so I'm just catching up on email now.

VMD already has separate code for 1, 2, and 3 point RMS fitting since
these don't meet the minimum criteria for the Kabsch method, but they
are based on simple geometric solutions (1-translation, 2-translate first
point, then rotate second, 3-translate first point, rotate second and third).
I could imagine these doing a poor job in some cases.

  John

On Fri, Mar 24, 2006 at 01:36:28AM +0100, Jan Saam wrote:
> Hi,
>
> Ah, duplicating atoms is a good hint, thanks!
> Nevertheless, I even saw it failing with more than 50 atoms...
>
> Well, but to cure the less than 4 atoms problem it would be nice if VMD
> would autodetect this case and internally duplicate these atoms for the
> RMS fit.
>
> Jan
>
>
> Brian Bennion wrote:
>
> >Hello,
> >
> >I replicated this problem as well using 1.8.3. However, if I remember
> >correctly the algorithm itself requires a minimum of 4 atoms to match.
> >
> >If you just duplicate one atom each for the two molecules the
> >alignment works just fine.
> >
> >Brian
> >
> >
> >On Thu, 23 Mar 2006, Visvaldas Kairys wrote:
> >
> >>Hi all,
> >>
> >>I am trying to use VMD to compute RMSD between selected residues, and
> >>for
> >>practical purposes I superimpose only the atoms under interest.
> >>Below is an example of molecules (in pdb format) which cause problem.
> >>
> >>molecule 1:
> >>
> >>CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
> >>ATOM 1 CA GLU A 1 -29.843 154.588 35.594 0.00 0.00
> >>ATOM 2 CA GLU A 2 -27.292 160.642 36.936 0.00 0.00
> >>ATOM 3 CA GLU A 3 -32.648 156.854 50.794 0.00 0.00
> >>END
> >>
> >>molecule 2:
> >>
> >>CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
> >>ATOM 1 CA GLU A 1 44.084 6.298 12.425 0.00 0.00
> >>ATOM 2 CA GLU A 2 39.046 2.420 14.373 0.00 0.00
> >>ATOM 3 CA GLU A 3 46.929 -0.875 26.932 0.00 0.00
> >>END
> >>
> >>If I open RMSD calculator extension, unselect backbone button
> >>and type "all" for atom selection, then click "Align",
> >>the molecules do not become aligned (it's pretty obvious), and "RMSD"
> >>is quite high. If I keep clicking "Align" and subsequent "RMSD",
> >>the position of atoms and RMSD keep changing.
> >>
> >>If I simply duplicate each atom in both of molecules above,
> >>yielding 6 atoms in each, the alignment and RMSD calculation proceeds
> >>correctly.
> >>
> >>I wonder if there is some formatting problem in my molecules or it is
> >>a bug.
> >>
> >>I had similar errors with two molecules consisting of 2 atoms. I
> >>didn't look
> >>carefully at other sizes of molecules, but big molecules seem to be OK.
> >>
> >>I am running VMD 1.8.4a22 on AMD64 Linux machine.
> >>
> >>Your help will be appreciated!
> >>
> >>Sincerely,
> >>
> >>Visvaldas Kairys
> >>University of Madeira
> >>Portugal
> >>
> >>
> >
> >************************************************
> > Brian Bennion, Ph.D.
> > Biosciences Directorate
> > Lawrence Livermore National Laboratory
> > P.O. Box 808, L-448 bennion1_at_llnl.gov
> > 7000 East Avenue phone: (925) 422-5722
> > Livermore, CA 94550 fax: (925) 424-5513
> >************************************************
> >
> >
>
> --
> ---------------------------
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> Germany
>
> +49 30 450-528-446
> saam_at_charite.de 

-- 
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