2.08                      *******************
                                  * MISSNG WRITE-UP *
                                  *******************
        
           MISSNG is a program to compare reflections in the main phased data
        set with those in other files, and output those reflections absent
        in the main file but present in the others. The output file thus
        contains candidates for phase extension. Usually the main (phased)
        data set is the output from PHASIT and contains all reflections which
        survived the cutoffs applied. The additional input files should include
        the complete native set, from which the "merged" data files input to
        PHASIT were created, but can also include other "phased" files (i.e.
        files containing phase probability distribution coefficients). In this 
        way additional reflections for which native amplitudes are available 
        (and possibly phase probability distribution coefficients) can be
        selected for phase extension via option 3 in BNDRY. The program is
        interactive, and prompts for the input and output file names, whether
        or not an additional "phased" file is to be included ( perhaps
        obtained from a partial structure via PHASIT, SF mode with IHLCF=1 and
        ISIGA=0 or 1), a d spacing cutoff, and the parameter file. The output
        file contains all additional reflections currently missing from the
        PHASIT file out to DCUT resolution for which native amplitudes are
        available. If the additional phased file was included, then for
        those reflections the phase distribution coefficients are also output
        and they will be used during phase combination in BNDRY. For those
        reflections without distribution coefficients, the calculated phase
        will be output in BNDRY as there is no phase information to combine
        with. The output file is generally called "extrfl.d". First the main
        phased file is read. Then if an additional phased file is to be used
        it is read and the reflections compared with those in the main file.
        The additional reflections are then written out along with the
        distribution coefficients. The native file is then read and the 
        indices are transformed to the standard asymmetric unit, and compared
        to all reflections previously encountered. Those reflections not
        yet utilized will then also be written to the output file, but will
        not contain distribution coefficients. 
        
                                   ***** FILES *****
        
        The input main phased file should be a PHASIT style output file (long 
        format, i.e. includes probability distribution coefficients). Only
        the indices are used, so that this file may contain either FM*FO and
        FO or FO and FC in the amplitude slots.

        If an additional phased file is used, it should also be a PHASIT style
        output file (long format), but it MUST contain FM*FO and FO in the
        amplitude slots as indices, FO and the distribution coefficients are
        to be used. It could thus be generated in PHASIT, SF mode with IHLCF=1
        and ISIGA=0 or 1, or in PHASIT, phasing mode.  
        
        The input complete native file can be one of three types. If the 
        filename ends with ".MU" or ".mu", then a XENGEN like MULIST is 
        assumed. Thus the file should contain records with
        
        H, K, L, RES, F, Sig(F), F+, Sig(F+), F-, Sig(F-), Iflag
        
        in format  (3I4, 1X, F6.4, 6(1X, F8.2) 1X, I2 ). 

        The "Iflag" parameter is not used and may be absent.
                
       
        If the filename ends with ".SCA" or ".sca", then a SCALEPACK
        file is assumed. After a variable number of header records
        (see the FILE FORMATS section), reflection records follow and
        contain

        H, K, L, I+, sig(I+), I-, sig(I-)

        in format (3I4, 4F8.1)

        Note the use of intensities rather than F's. The last two items
        in each record may be omitted. If present, they would be used
        only if I+ was not measured.
        
        
        If the file name does not end with ".MU", ".mu", ".SCA" or ".sca"
        each record is assumed to contain
        
        H, K, L, F, Sig(F)
        
        and is read in free format, i.e. each item must be separated by at 
        least one space or a comma. The indices must be INTEGERS and the F and 
        Sig(F) values REALS.
        
        
        In all cases the corresponding F values should be identical (or at
        least on the same scale) as those input to PHASIT.
       
 
        The output file is generally named extrfl.d for compatability with the 
        supplied template command procedures. Its records will contain H, K, 
        L, FNAT, A_B, C_D in format (3I4, F10.2, 2I12) where the distribution
        coefficients are packed two per word in A_B and C_D according to

        A_B = ( IFIX(A*100) + 16384 )*32768 + IFIX(B*100) + 16384

        C_D = ( IFIX(C*100) + 16384 )*32768 + IFIX(D*100) + 16384

        If distribution coefficients are not available the A_B and C_D values
        are zero.

        This file can be used for phase extension in option 3 of BNDRY.

        
        Note that MISSNG should always be used to prepare the file for phase 
        extension rather than some other program.  This is because MISSNG will 
        insure that the output indices correspond to the same standard 
        asymmetric unit as the rest of the program package.  If this is not 
        done, it is possible for redundant (symmetry related) reflections to 
        creep in to the data set.