BULK (CCP4: Supported Program)

NAME

   bulk - bulk solvent correction for translation search and rigid
   body refinement steps of AMoRe

SYNOPSIS

   prep_bulk
   bulking

DESCRIPTION

   BULK calculates a bulk solvent correction for the translation
   search and the rigid body refinement steps of the program AMoRe
   (Navaza, J. (1994). Acta Cryst. A50,157-163).

   Low resolution reflections are very useful for the translation
   search because they are less sensitive to errors in the model and
   in its orientation. However, at low resolution the contribution
   from the bulk solvent is quite significant and structure factors
   calculated from a macromolecular model alone cannot be compared
   with  experimental  values  if the bulk solvent correction is
   neglected.

   This program implements the bulk solvent correction using the flat
   solvent model (Jiang, J.-S. & Brünger, A. (1994) J.Mol.Biol., 91,
   201-228).

   IMPORTANT NOTE: Use this program if you have only one molecule in
   the asymmetric unit. The model has to be more or less complete. 

ALGORITHM

   See references below.
   The main steps of the procedure are:
    1. The molecular envelope (a binary function) is determined from
       the atomic model.
    2. Structure  factors  Fenv  are  calculated  as the Fourier
       coefficients of this function.
    3. The   structure   factors   Fsolv   are   calculated   as
       -ksol*exp(Bsol/(4*d*d))*Fenv For parameters ksol and Bsol the
       values ksol=0.35 e/A3, Bsol=50 A2 are recommended, but can be
       altered (see below).
    4. The structure factors Fsolv are added to the structure factors
       Fatom calculated from the atomic model to obtain the corrected
       structure factors Fcorrected=Fatom+Fsolv.
    5. The  corrected structure factors are used, instead of the
       structure factors calculated from the atomic model, in the
       translation search and rigid body fitting.

   To run the procedure 'BULK' a user has to:
    1. execute the 'tabling' procedure of AMoRe
    2. prepare the file 'prep_bulk.inp' with the following content:

          a.pdb         ! name of the file with model coordinates (the
 same as
                        !  used for the 'tabling' step)

          search.tab    ! name of the file with the structure factors
from
                        ! AMoRe's 'tabling' procedure

          tab.log       ! name of the log file of AMoRe's 'tabling' pr
ocedure

          search.tabs   ! name of the file with the bulk-solvent-corre
cted
                        ! structure factors (this file will be created
 by the current
procedure)

          bulking.inp   ! name of an intermediate file of control para
meters for
                        !  'bulking';
                        ! this file will be created by the program pre
p_bulk (see sect
iot 4)

           0.35         ! value of ksol

          50.0          ! value of Bsol

           1.0          ! value of the solvent radius used for the sol
vent mask
                        !  calculation

       Alternatively, these parameters can be given directly to the
       program prep_bulk, as in the example linked below.
    3. issue consecutively the two following commands:

          prep_bulk < prep_bulk.inp

          bulking < bulking.inp

       The output file 'search.tabs' with bulk-solvent-corrected
       structure factors can be used for the translation search and/or
       for rigid-body refinement.

INPUT AND OUTPUT FILES

  a.pdb

   PDB file of search model, as used in Amore tabling.

  search.tab

   Output tabling file from Amore.

  tab.log

   Log file of Amore tabling step.

  search.tabs

   Output file from bulking. This file can be used in Amore in place
   of the original search.tab

EXAMPLES

  Runnable example

   bulk.exam - this is a very simple example for testing purposes. For
   scientifically more interesting examples, see references below.

MEMORY ALLOCATION

   Program is written in standard FORTRAN 77, so it uses static memory
   allocation. In the case of problems, the maximal array dimensions
   can be changed by setting the parameters:

                     maxNgrid=20000000
                      maxrefl=3000000
                       maxatm=100000

   right at the beginning of the source file bulking.f

SEE ALSO

   amore

REFERENCES

    1. A. Fokine, G. Capitani, M.G. Grutter, A. Urzhumtsev, J. Appl.
       Cryst. 36 352-355 (2003)
    2. A. Fokine and A. Urzhumtsev, Acta Cryst. A58 72-74 (2002)
    3. A. Fokine and A. Urzhumtsev, Acta Cryst. D58 1387-1392 (2002)

AUTHORS

   A. Fokine, A. Urzhumtsev: University of Nancy 1, France
   G. Capitani, M.G. Grutter: University of Zurich, Switzerland