BULK (CCP4: Supported Program)

NAME

SYNOPSIS

DESCRIPTION

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' procedure
   
             search.tabs   ! name of the file with the bulk-solvent-corrected 
                           ! structure factors (this file will be created by the current 
   procedure)
   
             bulking.inp   ! name of an intermediate file of control parameters for 
                           !  'bulking'; 
                           ! this file will be created by the program prep_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 solvent 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

search.tab

tab.log

search.tabs

EXAMPLES

Runnable example

MEMORY ALLOCATION

                     maxNgrid=20000000
                      maxrefl=3000000
                       maxatm=100000

SEE ALSO

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