2.10 *******************
* MRGBDF WRITE-UP *
*******************
MRGBDF is a program to create coefficients for Bijvoet difference
or cross Bijvoet difference Fourier synthesis calculations, i.e. try
to determine anomalous scatterer locations from phase information
obtained from one or more other derivatives. It can also be used
simply to search for additional anomalous scatterer sites once initial
estimates of protein phases become availabler, although the
"difference coefficients" file output from PHASIT may be better suited
in this case since one can then also subtract out the heavy atoms
already present in the model, and also generate a "calculated"
Patterson for comparison with the "observed" one. The program is
interactive and prompts for the names of the input and output files,
and a d spacing cutoff. A merged file input may be either a "native
anomalous scattering" or "derivative anomalous scattering" type file
(see PHASIT write-up), and the user will be prompted to identify the
type. The output file can be used in FSFOUR with MAPTYP=8 to compute
the Bijvoet-difference Fourier synthesis. If the input Bijvoet pair
file is one of the "merged" data files originally input to PHASIT,
then the coefficients output can be used to compute a Bijvoet
difference Fourier to identify additional anomalous scatterer sites
which may have been overlooked. In that case it is not a "cross"
Fourier but a straight Bijvoet difference Fourier. If the Bijvoet pair
file input corresponds to a new derivative, then the coefficients can
be used for a "cross" Bijvoet difference Fourier to reveal the
locations of anomalous scatterers in the new derivative. The program
is also useful to determine whether the heavy atom hand designation
agrees with the anomalous scattering data. When everything
is consistent maps computed should reveal POSITIVE peaks at the
appropriate anomalous scatterering sites for all Bijvoet pair data
sets. If the hand for the heavy atoms used in phasing is inconsistant,
then the map will reveal NEGATIVE peaks at the true sites, i.e. those
related to the input (incorrect) set BY A CENTRE OF SYMMETRY.
Program PSRCH can be used to list the strongest peaks (both positive
and negative) in the map, and program HNDCHK can be used to aid in
hand determination by examining the density precisely at any arbitrary
location. In general, one could phase the data using both possible
hands and check the results as just described.
If derivative Bijvoet differences are used, The program will prompt
the user to supply values for derivative to native scale and delta B
factors, if rescaling is requested. If utilized, this option enables
the user to change the scaling originally carried out in CMBANO, to
reflect the fact that additional scattering power is present in the
derivative data set. In that case the new scaling parameters should be
those determined from PHASIT in phase refinement mode.
***** FILES *****
The input Bijvoet pair file is identical (in form) to one of the
"merged" data files input to PHASIT. Each record should contain either
H, K, L, F+, SIG(F+), F-, SIG(F-)
or
H, K, L, FP, SIG(FP), FPH+, SIG(FPH+), FPH-, SIG(FPH-)
This file refers to the new derivative which is to be solved, or to a
current data set for which one wants to search for additional
anomalous scatterer sites. It is read in free format.
The input protein phase file can be one of two types. Usuallly it will
be the last output file from BNDRY, or an output file from PHASIT (in
protein phasing mode). In general, it should contain the best
available phases. The form of the file would then be identical to that
output from BNDRY or PHASIT (in protein phasing mode). It is also
possible however, to input a protein phase file which contains records
with the "short" reflection file form (only h,k,l,fo,fc,phi) as
generated by GREF or PHASIT (in structure factor calculation mode,
IHLCF=0). In that case there is no figure of merit present, thus FOM=
1. is used during generation of the output coefficients. This would be
the case if the protein phases come from a complete (or partial)
protein model based structure factor calculation. The program can
automatically determine which type of file was input. Note however,
that a phase file generated by GREF should NOT be used here unless
GREF was used to compute structure factors from a complete protein
model.
The output file is binary and is suitable for input to FSFOUR.
Each record contains
H, K, L, FOM*F+, FOM*F-, PHI+
where the indices are INTEGERS, the other quantities REALS and PHI+ is
in degrees.
PHI+ = PHICALC for + type output file.
PHI+ = -PHICALC for - type output file.
The figure of merit and PHICALC come from the phased file while
F+ and F- come from the Bijvoet pair data file. The Bijvoet difference
Fourier should be computed with coefficients
-i * (FOM*F+ - FOM*F-) * exp (i * PHI+)
where the -i factor is applied after expansion to a hemisphere, and
during the expansion, care is taken to insure that the differences are
"flipped" if putting the reflection into the desired hemisphere
involves an inversion. This is taken care of automatically in FSFOUR
if MAPTYP=8 is selected.