BULK (CCP4: Supported Program)
- 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:
- The molecular envelope (a binary function) is determined from the atomic
- Structure factors Fenv are calculated as the Fourier coefficients of this
- 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).
- The structure factors Fsolv are added to the structure factors Fatom
calculated from the atomic model to obtain the corrected structure factors
- The corrected structure factors are used, instead of the structure factors
calculated from the atomic model, in the translation search and rigid
To run the procedure 'BULK' a user has to:
- execute the 'tabling' procedure of AMoRe
- 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
! this file will be created by the program prep_bulk (see sect
0.35 ! value of ksol
50.0 ! value of Bsol
1.0 ! value of the solvent radius used for the solvent mask
Alternatively, these parameters can be given directly to the program
prep_bulk, as in the example linked below.
- 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
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
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
right at the beginning of the source file bulking.f
- A. Fokine, G. Capitani, M.G. Grutter, A. Urzhumtsev,
J. Appl. Cryst. 36 352-355 (2003)
- A. Fokine and A. Urzhumtsev, Acta Cryst. A58 72-74 (2002)
- 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