VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 14 2002 - 11:35:17 CDT

Dear Vlad,
  We have fixed a number of bugs that existed in VMD 1.7.x with regard to
RMSD calculations. Can you try the VMD 1.8 version available on the VMD
web site and let us know if you still have this problem? I know that we
also fixed some other very rare/subtle bugs in the "measure" commands.
If you're curious, here is the list of bugs we've already fixed in VMD 1.8
so far:
  12, 20, 74, 77, 138, 144, 147, 149, 179, 180, 182, 183, 184,
  190, 197, 198, 201, 202, 208, 209, 210, 211, 212, 213,
  214, 215, 218

You can lookup detailed info on these bugs from our development tracking
page here:
  http://www.ks.uiuc.edu/Research/vmd/development.html

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 14, 2002 at 05:46:48PM +0200, Vlad Cojocaru wrote:
> I noticed a problem with the rmsd calculation. I am using 1.7.1 version.
> If I am calculating the rmsd of two structures using the following script
>
> logfile vmd.log
> mol load pdb rna_ion_wat_mdeq0.pdb
> mol load pdb rna_ion_wat_0.pdb
> set sel1 [atomselect 0 "resid 1 to 17"]
> set sel2 [atomselect 1 "resid 1 to 17"]
> measure rmsd $sel1 $sel2
> set tm [measure fit $sel1 $sel2]
> set move_sel [atomselect 0 "all"]
> $move_sel move $tm
> #mol modselect 0 0 {resid 1 to 17}
> #mol modselect 0 1 {resid 1 to 17}
>
> it gives for the 2 structures that are almost perfectly overlaid a value
> of 3.7... obviously abnormal since I calculated the same thing with many
> other programs and the value is 0.267. I must say that this script is
> working sometimes pretty fine with other structures. Does anybody have
> any ideea what might happen here?
> Thanks a lot,
> 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
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078