BULK (CCP4: Supported Program)


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




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.


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 
              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.



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


Output tabling file from Amore.


Log file of Amore tabling step.


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


Runnable example

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


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:


right at the beginning of the source file bulking.f




  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)


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