2.04 *******************
* MAPINV WRITE-UP *
*******************
PURPOSE- To calculate three dimensional Fourier coefficients
(structure factors) when given an electron density
map and control cards.
This program will calculate structure factors by using a
multivariate variable radix fast Fourier transform algorithm to invert
an electron density map. The program is fully general so that all
space groups can be handled. It is assumed that the input map was
prepared by program FSFOUR. Structure factors may be calculated for
reflections in the following range:
h .ge. -NX/2 and h .lt. NX/2
k .ge. -NY/2 and k .lt. NY/2
l .ge. 0 and l .lt. NZ/2
where NX, NY, NZ are the number of grid points along the a, b, and c
axes, respectively, in the input map.
INPUT DATA (UNIT 5)
CARD 1 PAMFIL (free format)
PAMFIL = Name of input file containing cell and symmetry
parameters.
CARD 2 TITLE (free format)
TITLE = anything
CARD 3 MAPFIL (free format)
MAPFIL = Name of input map file.
CARD 4 SFOUT (free format)
SFOUT = Name of output structure factor file.
CARD 5 IPRNT, IPAIR, HMIN, HMAX, KMIN, KMAX, LMAX (free format)
IPRNT = 0 for no printing of structure
factors.
= 1 for printout
IPAIR = 0 for no pairing of calculated
structure factors with observed
data.
= 1 to combine calculated structure
factors with observed data
(supplied on auxilliary file) and
output R factor to the line printer
= 2 same as 1, but a separate file with
the combined data is also written.
HMIN =
limiting values defining range of
HMAX =
indices for which structure factors
KMIN =
will be calculated
KMAX =
(LMIN is always 0)
LMAX =
CARD 5A AUXINP (free format)
***** This card should be included ONLY if IPAIR > 0 *****
AUXINP = Name of input file containing auxilliary structure
factors for scaling.
CARD 5B AUXOUT (free format)
***** This card should be included ONLY if IPAIR = 2 *****
AUXOUT = Name of output file to contain calculated structure
factors scaled to (and paired with) the auxilliary
structure factors.
CARD 6 SC, F000, IMOD, IRHOMN (free format)
SC = scale factor applied to calculated
structure factors (see below).
If 0. defaults to 1.
F000 = total number of electrons in the unit
cell (see below).
IMOD = 0 for no modification of map prior to
transformation
= 1 to modify map prior to transformation
according to input criterion
=-1 same as 1 but the resulting density
is also squared prior to transformation.
IRHOMN = modification criterion (applied if
IMOD .ne.0). If (rho input + IRHOMN) < 0,
rho will be reset to 0. If F000 is
supplied, IRHOMN is automatically set to
correspond to non-negativity of electron
density.
********** NOTES ON THE PROGRAM **********
The input map file MAPFIL is assumed to have been generated with
program FSFOUR. It is binary, terminated with an end of file, and
after a few header records, contains the electron density map
represented as records (of integers) along x. y is the slowest varying
coordinate.
All calculated structure factors within the index range specified will
be output to file SFOUT. Note that this may include redundant
(symmetry related) as well as systematically absent reflections, if
they they fall within the specified index range. The output file is
binary, with records of H,K,L,FCALC,FCALC,PHI and is terminated by an
end of file. H,K and L are INTEGERS whereas FCALC and PHI are REALS.
PHI is in degrees. Note that FCALC is duplicated within each record so
that the file structure is consistant with the input required by
program FSFOUR.
If IPAIR > 0, then in addition to file SFOUT, an input file AUXINP of
observed structure factor amplitudes will be paired with the
corresponding calculated amplitudes and phases, and the combined data
used in one cycle of least squares refinement of a scale factor. The
resulting R factor between observed and calculated amplitudes is then
output to the lineprinter. Note that the input reflection data on file
AUXINP is restricted to the same range of indices as the calculated
data. If input values fall out of bounds they will be ignored.
Therefore, if data were collected with L negative, it will have to be
transformed by symmetry before it can be used successfully on file
AUXINP.
If IPAIR = 2, the results are identical to those obtained with IPAIR =
1, except that the combined (and rescaled) data is also output to a
separate file AUXOUT. The new file is of the same form as SFOUT, but
with records consisting of H,K,L,FOBS,FCALC,PHICALC for only those
reflections which were input on file AUXINP.
***** SCALING THE DATA *****
It is often desirable to control the scale of the calculated structure
factors. If the input electron density map was generated from
structure factors which are related to an absolute scale by:
F(input to FSFOUR) = k * F(absolute)
then k should be input for SC to obtain calculated structure factors
on an absolute scale. If sc= 0. (or 1.), then the calculated structure
factors will be on the same scale as those used to generate the map
(unless IMOD = -1, in which case they will be much larger). Note that
this scaling applies only to the output on file SFOUT (and the
lineprinter, if IPRNT .ne.0). If IPAIR .eq. 2, then the calculated
structure factors on file AUXOUT will always be scaled for best
agreement with those supplied on file AUXINP.
***** MODIFYING THE MAP *****
The following applies only if IMOD .ne. 0. Inclusion of F000 will
result in imposing non-negativity of electron density everywhere in
the map prior to inversion, provided SC is reasonably well known. If
SC is unknown, then F000 and SC on card 3 should be zero and IRHOMN
should be input to control the type and degree of modification.
Intelligent use of this parameter would then require knowledge of the
input map values prior to running the job. IRHOMN should be equal to
F000/V on the same scale as the input map. If IMOD = -1, IRHOMN is
first added to each density value, resulting values below zero are set
to zero, and each value is then squared prior to Fourier
transformation. This is equivalent to imposing non-negativity,
followed by one cycle through the tangent formula. Phases can
therefore be tangent formula refined or extended.
***** FILE REQUIREMENTS *****
MAPFIL - input map file, binary, as output by program FSFOUR
SFOUT - output file with all calculated structure factors,
binary, six word records as described earlier
AUXINP - auxilliary input structure factor file (required only
if IPAIR .ne. 0), binary, six word records in same form
as SFOUT (only H,K,L and FOBS are used)
AUXOUT - output auxilliary structure factor file, binary, six
word records as described earlier.