ANALYZE_MIR: Analyzing an MIR dataset
ANALYZE_MIR is a routine to calculate difference Pattersons and anomalous difference Pattersons for an MIR dataset, to calculate correlation coefficients among them all, and to set up a "solve_mir.script" file that can be used to run SOLVE on the dataset. You usually do not have to worry about this routine at all because it is ordinarily called right after running SCALE_MIR for automatic structure determination. It is ordinarily followed by running SOLVE with the solve_mir.script file written out by this routine or by using the keyword "SOLVE" after running this routine.
ANALYZE_MIR assumes that you have a datafile ("mir_fbar.scl") that contains Fnat, sigma, and (Fbar,sigma,DelAno,sigma) for each derivative of MIR data. That is, there are exactly 2 columns of data for the native and 4 data columns for each derivative. This is a dorgbn file. It is ordinarily created by SCALE_MIR, but you can create your own if you like.
To run ANALYZE_MIR, you need to input your standard setup file ("solve.setup"), and the name of the mir datafile. ANALYZE_MIR will calculate origin-removed difference Pattersons for all isomorphous and anomalous differences. These maps are all compared to each other and the correlation coefficients are displayed in a table. In a typical MIR experiment the anomalous and isomorphous difference Pattersons have correlations with each other on the order of 0.0 to 0.2 or so (pretty low, so don't be worried).
ANALYZE_MIR writes out a script file "solve_mir.script" that you can use to go on with the SOLVE routine to solve this mir structure. You can edit this script file to modify it if you like or you can run it as is. You can also go right on with SOLVE by adding the command "SOLVE" after "ANALYZE_MIR".
Please note that there is a slight difference between running ANALYZE_MIR right after SCALE_MIR and in a separate session. If you run them right after each other, you should input all the information about each derivative at once, as in the sample script for automatic analysis of MIR data. (If you wanted to input information about derivative #1 in two places in your script file, you would need to use the keyword "gotoderiv 1" the second time. You can avoid this by putting all the information for derivative #1 together.)
A typical input script for ANALYZE_MIR follows:
!--------------------------Run ANALYZE_MIR---------------------------------
@solve.setup ! standard information for this crystal
mirfbarfile mir_fbar.scl ! input dorgbn file with Fnat,sig, and
! (Fbar,sig,Delano,Sig) for each wavelength
logfile analyze_mir.logfile ! write out most information to this file
derivative 1 ! derivative #1 information is to follow
label deriv #1 Hg ! label for deriv 1
atomname HG ! this is an HG derivative
derivative 2
label deriv #2 Iodine
atomname I-
ANALYZE_MIR !analyze all the Pattersons and
!write solve_mir.script
!-----------------------------------------------------------------------------
Keywords for ANALYZE_MIR:
LOGFILE xx.logfile log file for output will be xx.logfile
mirfbarfile xx.scl input dorgbn file with Fnat, sig, and
(Fbar,sig,Delano,Sig)
for each wavelength will be xx.scl
[Default="mir_fbar.scl"]
SCRIPTFILE xxx Output script file containing instructions
for running SOLVE written to xxx
[default="solve_mir.script"]. Starting SOLVE with
this script is equivalent to following
ANALYZE_MIR with SOLVE.
derivative n derivative number (n=1,2,3...) for values
to be entered next of atomname and label
label xxxx xxx is a label for this derivative
ATOMNAME XXXX XXXX is the atom name of the atoms in
this derivative. This name can be in
SOLVE's database or you can
enter it using the NEWATOMTYPE keyword.
PLEASE NOTE: the f' and f" values assumed
by SOLVE are for Cu Kalpha radiation (1.54 A).
If you collected your MIR data at a synchrotron
then you will want to define a new atom type
with the appropriate values of f' (fprimv) and
f" (fprprv). See the HEAVY or SOLVE keyword
lists for entering a NEWATOMTYPE.
The atom types recognized by SOLVE are:
S, Fe, Cu, Se, Ru, Rh, Pd,
Te, I, Xe, Sm, Eu, Gd, Tb, Ho,
Yb, Hf, Ta, W, Re, Os, Ir, Pt,
Au, Hg, Pb, Th, and U
NSHELLS n Number of shells for analysis is n
[default=10]