VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Thu Feb 13 2003 - 19:33:38 CST

Hello,

   The aligntool extension is designed for proteins, and uses both sequence and
structure similarities to perform the alignment. Much more commonly
encountered than this are: alignments of structures based only on
structure, which just find a rotation+translation to minimize the RMSD betwen
two sets of atomic coordinates. VMD offers tools to do this:

   See insructions on "measure fit", "measure rmsd" and related commands at

 http://www.ks.uiuc.edu/Research/vmd/current/ug/node181.html

  especially "RMS and Scripting"

http://www.ks.uiuc.edu/Research/vmd/current/ug/node183.html

   You can use these tools for proteins, DNA, or anything else you have loaded
into VMD.

                                   Cheers,
      
                                   Barry

On Thu, Feb 13, 2003 at 03:43:44PM -0800, Ioana Cozmuta wrote:
> Hi vmd users,
>
> Is the aligntool specially designed only for proteins? I am trying to
> align two structures of nucleic acids and thought could use this tool to
> calculate the RMSD. But I get an error saying that there are no alpha
> carbons found in the files. So I assumed it does not work with other
> structures than proteins...
>
> Thanks,
> Ioana 

-- 
Barry Isralewitz   Theoretical and Computational Biophysics Group, UIUC  
Beckman 3121   Office Phone: (217) 244-1612  Home Phone: (217) 337-6364
email: barryi_at_ks.uiuc.edu      http://www.ks.uiuc.edu/~barryi