VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Fri Aug 16 2002 - 08:56:28 CDT

Hi Vlad,

Would it be possible for you to send us the two structures you are aligning
so that we can determine what the problem might be? It wouldn't even have
to be the entire structure if you'd prefer; just the atoms used to calculate
the fitting matrix would be sufficient. We've been using rmsd for some time
now and had figured we'd gotten the code pretty reliable, but this could be
the test case that uncovers a bug...

Thanks,
Justin

On Fri, Aug 16, 2002 at 11:33:55AM +0200, Vlad Cojocaru wrote:
> Hi!
> I am sorry to tell you but when it comes to rmsd fit the VMD 1.8a21
> gives the same results as 1.7.1. So, for instance for two structures
> that overlay almost perfectly the rmsd value is something like 3.42
> ....imp[ossible no??
> Bets regards,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>
> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys