A
program for Fourier maps calculations.
JGP JRC 2004
Scope
The
program Fourier calculates the
scattering density inside the unit cell of a crystal of whatever symmetry. The GFourier allows to create and visualizate the
results of Fourier program using a
menu-driven interface with the help of the mouse and few keyboard input.
The program Fourier calculates the scattering density inside the unit cell
of a crystal of whatever symmetry. It uses a Fast Fourier Transform
(FFT)
subroutine to accelerate the calculation of the following expression:
Where V is
the volume of the unit cell. H is a reciprocal lattice vector, r
is a vector position inside the unit cell, and F(H) are complex Fourier coefficients used to perform different
types of Fourier syntheses. The units of are those of F(H) divided by those of V. For instance, if F(H) are given en electron units (usual absolute units for X-ray
diffraction) and V in
,
is calculated
as Number-of-Electrons/
.
Running the program
Invoking the program:
Local_Prompt> fourier [input_file]
where the input file is the control for the program.
Also you need a file containing the hkl’s and structure factors. The extension
for both files are inp and fou respectively. If Fourier runs properly il will output up to two
files:
CODE.out General
output file
CODE.bin Binary
file containing the scattering density inside the unit cell.
The program GFourier
allows to create from the scratch an input control file CODE.inp for Fourier
using just a menu-driven interface with the help of the mouse and few keyboard
input.
The
input control file is totally free format. It is a command-driven-like file.
All commands and keywords are case insensitive. Empty lines are allowed and if
the symbol "!" appears as the first character, the line is considered
as a comment.
There
are only 13 commands that are explained below (for a sake of clarity we give
here the commands and keywords in upper-case):
ATOM
e.g. ATOM
Label X Y Z
[occ]
This
command is optional and the maximum number that can be input at present is 500.
Label is a string (of 4 characters
max) representing the name of the atom and X
Y Z are three real numbers representing the fractional coordinates. occ is the occupation number. This
parameter is optional.
The
atoms are not used inside Fourier. They are given optionally only for
graphic representation purposes. Fourier put this information in the output binary
file that is read by GFourier.
Example: ATOM Ba
0.5000 0.5000 0.5000
CELL
e.g. CELL a b c alpha beta gamma
The
command CELL is followed by the six
real numbers defining the metrics of the unit cell. Usually a,b,c are in angstroms and alpha,beta,gamma in degrees.
END
This command tells the
program that the lines below are not to be taken into account.
FILE
e.g. FILE
KeyWords NameFile
The command FILE provides information about files
to the program. NameFile is the name
of a file. It may include the full path. The values of Keywords are:
FOU
The structure factors file
name is provided in NameFile.
ATOM
The name of an optional atom file (only the ATOM
command is recognized inside) is provided in NameFile
BIN
The name of the binary file is provided in NameFile.
NameFile can be absent if BIN and ATOM are given. In this case
the name of the file is the same as the name of the input control file with
extensions ".bin" and
".atm".
Examples: FILE fou
myfile.fou
FILE ATOM
my_atoms.atm
FILE
bin
FOURIER
e.g. FOURIER KeyWords
This
command tells to the program what kind of Fourier synthesis have to be
calculated. At present, the possible values of KeyWords are:
PATT FOSQ
Patterson Map using observed squared structure factors
PATT FCAL
Patterson Map using calculated squared structure
factors
FOBS
Fourier Map using observed structure factors and
calculated phases
FCAL
Fourier Map using calculated structure factors and
phases
DIFF
Difference Fourier Map
AABB
User supplied real and imaginary parts of the Fourier
coefficients
Examples: FOURIER PATT
FOSQ
FOURIER
DIFF
FORMAT
e.g. FORMAT kw1
kw2 kw3 kw4 ...kw9
Where
kw(i) are keywords representing one
of the following items:
H: h-index
K: k-index
L: l-index
A: Real part of the structure factor (or of the
user-supplied Fourier coeff.)
B: Imaginary part
Fo: Observed structure factor
Fc: Calculated structure factor
Phase: Phase of the structure factor in degrees.
SigFo: Standard deviation of the observed structure factor.
Tells
the program the order in which appear the different items in the Fourier file
specified by FILE FOU.
Examples: FORMAT h k l
A B
FORM h k l
Fo Fc Phase
Form A B
Fo h k l
F000
e.g. F000 value1 [value2]
Gives
the value of F(000) (value1) and a scale factor (value2) for all map. The default
values are value1=0.0000, value2=1.000
Example: F000 822
1.0
GRID
e.g. GRID
nx ny nz
User-supplied
grid values for calculating the scattering density. By default the program
calculates automatically the three integer values nx, ny and nz.
Example: GRID 20 20 25
LIST
e.g. LIST Keywords
This
command tells to the program output additional information. At present, the
possible values of KeyWords are:
ATOMS
List of atoms in the unit
cell.
DIST value1 value2
List of distance of the peaks between value1
and value2. In default, value1 =
1.000, value2 = 2.5 Å.
Example: LIST atoms
LIST dist 1.8
2.25
REFLEC
e.g. REFLEC KeyWord Value(s)
Where
KeyWord is one of the items SRAN, SMIN, SMAX, SIGM and Value(s) is one or two (only for SRAN) real numbers.
This
command instructs the program about the limits of
Fourier calculation.
Examples: REFLEC SRAN
0.0 0.88
reflec SMAX 1.2
Reflec SMIN 0.2
SCAN
e.g. SCAN npeaks
This
command activates the peak search subroutine. The program look for the
coordinates of the highest "npeaks" peaks in the asymmetric unit of
the mapThese are
repeated for the first "npeaks" peaks found. Symmetry equivalent peaks are not included.
Example: SCAN 10
SPGR
e.g. SPGR Space_Group
The
command SPGR tells to the program
that the string Space_Group is the Hermann-Mauguin symbol for the space group.
The symbol must be given using a space before the symbol corresponding to a
symmetry direction. Following the International Table descriptions, choice 1
can be introduced by adding “:1” to
Hermann-Mauguin symbol (choice 2 is in default) and for Rhombohedral axes “:R” (hexagonal axes are in default).
Examples: SPGR
P n m a
SPGR P 41/m
SPGR
P m m n:1
SPGR
R 3:R
The
program uses the symbol to generate the full set of symmetry operators that are
used to expand the reflection indices. It is wise to verify that the reduced
set of symmetry operators are correctly generated.
e.g. TITLE comment
The
command TITLE tells the program that
comment should be used as a title.
Example: TITLE Fourier Difference Map for CarbaDiazepine
Javier Gonzalez
- Platas
Instituo de Bioorgánica “Antonio González” & Dpto.
de
Universidad de La Laguna, Tenerife, SPAIN
Tel: (34) 922 318317, Fax: (34) 922 318320
e-mail: jplatas@ull.es
Juan Rodriguez
- Carvajal
Laboratoire Leon Brillouin (CEA - CNRS)
CEA / Saclay, 91191 Gif sur Yvette Cedex, FRANCE
Tel: (33) 1 6908 3343, Fax: (33) 1 6908 8261
e-mail: juan@bali.saclay.cea.fr