VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Thu Mar 23 2006 - 18:36:28 CST

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