
NORMA normal mode fiting of crystal structures into EM densities using URO and NMA
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Karsten Suhre <mailto:karsten.suhre@igs.cnrs-mrs.fr> , Wed Oct 20 2005


This directory contains :

* The IBDV EM density map in NEWEZD format 

  map_odd.ezd

  REF: Coulibaly F, Chevalier C, Gutsche I, Pous J, Navaza J, Bressanelli S, Delmas B, Rey FA., 
       The birnavirus crystal structure reveals structural relationships among icosahedral viruses.,
       Cell 2005; 120:761-772.

  NOTE: This dataset has been kindly made available for use within the educational context
        of NORMA only. This dataset is NOT in the public domain.
        For further copyright details, please contact :

        Jorge Navaza
        Laboratoire de Virologie Moléculaire & Structurale
        UMR 2472 CNRS - 1157 INRA Bât. 14B
        1 Avenue de la Terrasse
        91198 Gif-sur-Yvette Cedex
        France
        email: jnavaza@vms.cnrs-gif.fr
        tel: 01 69 82 38 43
        fax: 01 69 82 43 08


* The initial model (as a trimer), prepositioned into the EM map:

  1WCD.reo.pdb

  REF: as for the EM map (see above)


* The symmetry file for URO in two formats and the viewing position for O (see URO documentation)

  sym
  gs.real
  gs.sym
  

* A shell script to call URO from NORMA via the script func.sh

  go.URO.minimize

* To setup the case IBDV case, do the following:

  # setup URO and move files to ./d
  csh $URO/setup
  mv sym gs.sym gs.real map_odd.ezd 1WCD.reo.pdb ./d

  # test URO by running func.sh by hand (this first run may take a while since
  # the normal modes will have to be calculated)
  # Don`t forget to set the PATH to NMA and NORMA !
  sh ./func.sh



see also :
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http://www.igs.cnrs-mrs.fr/elnemo/NORMA/

