
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 19 2005


This directory contains :

* The GroEl EM density map in NEWEZD format 

  GroEl.ezd

  REF: De Carlo S, El-Bez C, Alvarez-Rua C, Borge J, Dubochet J.,
       Cryo-negative staining reduces electron-beam sensitivity of vitrified biological particles.,
       J. Struct. Biol. 2002; 138:216-226.


* The initial model, open conformation, prepositioned into the EM map:

  1aonA.pdb (open form)

  REF: Ranson NA, Farr GW, Roseman AM, Gowen B, Fenton WA, Horwich AL, Saibil HR.,
       ATP-bound states of GroEL captured by cryo-electron microscopy.,
       Cell. 2001; 107:869-879.


  Aa.1SX3.pdb (closed form)

  REF: Chaudhry C, Horwich AL, Brunger AT, Adams PD.,
       Exploring the structural dynamics of the E.coli chaperonin GroEL using 
       translation-libration-screw crystallographic refinement of intermediate states.,
       J. Mol. Biol. 2004; 342:229-245.


* The symmetry file for URO in two formats and the viewing position for O (see URO documentation)
  sym
  gs.sym
  symlist
  gs.real


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

  go.URO.minimize


* A shell script that computes the function to minimize - it will be called by NORMA.f
  and read a file func.in as input; it should output a file func.out containing value
  of the function to be minimized (Q*1000) 

  func.sh
  func.in  ( this file will be overwritten - it is only provided for testing purposes)


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

  # setup URO and move files to ./d
  csh $URO/setup
  mv sym gs.sym gs.real symlist GroEl.ezd 1aonA.pdb Aa.1SX3.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


*  Check file func.log. If all works correctly, the following files will have been generated: 

  func.log          # func.sh output
  pdbmat.log        # NMA pdbmat log file
  diagrtb.log       # NMA diagrtb log file
  proj_modes.log    # NMA proj_modes log file

  1aonA.eigenfacs          # the normal modes in ASCII format
  1aonA.proj_modes_bin.IO  # the normal modes in binary format (will be regenerated if deleted)

  func.out          # 1000*Q ; should be something close to  32661  in this first example

  ./d/1aonA.NMApert.pdb    # the normal mode perturbed PDB file

  ./RUN.minimize    # URO files (logs/results)



* Go to ./RUN.minimize and run O from here - check if all looks correct.

  cd ./RUN.minimize
  xterm -e ono &      # hit RETURN a number of times, then type "@ono" to load the map



* Now it is time to run NORMA. Adapt the parameter file NORMA.inp, e.g for a fast one-modal fit use

&PARAM
 NDIM    =           1,
 DY      =    200.0000,
 NITER   =          50,
 TEMPTR  =     50.0000,
 NANNEAL =           0,
 NROUND  =           1,
/


* To compute an animated PDB file for a fit modify line= in gen_pert.sh 
  based on the final solution proposed by NORMA, 
  e.g. for monitor=  21516.000000, p=  7    575.000000
  type:

    ./gen_pert.sh 7 575.


  This will yield a file named anim.pdb that can be viewed as animation using VMD:

    vmd anim.pdb


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

