Abstract from: 4-files.txt [dirdif manual chapter 4]       2 June 2008
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This is a summary: for more details, see dirdif/docs/4-files.txt 


The filename dictates the contents and the format of the file.
Filenames sometimes are represented (in programs, documents, and
output listings) by capitals. The actual file names are in lower case , 
but some concatenate the name to the compound code ( denoted CCODE ).

Listing file lis1
-----------------
The file Lis1 gives the most important information on the DIRDIF run. 
 
Atomic parameter file atoms
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The input and output atomic parameter files of the DIRDIF system are:
- atoms file: input to most programs, replaced by output parameters,
- CCODE.ins and CCODE.res : SHELX control data files 
 
The atoms file consists of the following records (keywords and data):
atoms    CCODE    more-info       (CCODE = compound code)
ATOM     atomname   x  y  z       (x,y,z: fractional atomic coordinates)
                                  (one atom / record, as many as needed)
REMARK   comments                 (optional, as many as desirable)
END                               (last record)
 
The ATOM records may have a site occupancy factor (sof = 1.00) and an 
isotropic temperature factor (B):
ATOM        atomname   x  y  z   sof   B
 
At the end of a structure solving run, the program AT2X converts
the output atoms file to a SHELX type file: CCODE.res .

File atmod with the model parameters input to the program ORIENT
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The atmod file has the same structure as the atoms file.
Possible header records are:
ATMOD    MCODE    more-info                 (MCODE = Model code)
ATMOD    MNUM     MCODE                     (MNUM = Model number)
ATMOD    MCODE    MCELL a b c alpha beta gamma
ATMOD    CART
ATMOD    MCODE CART MNUM
ATOMS    CCODE                             (using cell of present CCODE)
 
ATOM records with atomic parameters  (one atom / record, as many records
as needed) contain either
     fractional coordinates:             ATOM   atomname    x  y  z
     or Cartesian coordinates:           ATOM   atomname    X  Y  Z


Atomic parameters of a known molecular model can be retrieved from the
DIRDIF-ORBASE fragment file at an interactive terminal session. For
larger structures these fragments may be too small. The Vector Search
method can often be employed more powerful if you retrieve molecular
models from your own solved structures, or from the literature, or by
molecular modelling. It is convenient to prepare an atmod file in
advance, and modify the model (delete, rename, and add atoms)
interactively.
 


Crystal data file crysin
------------------------
 
crysin :     primary crystal data = standard DIRDIF input file.
Other optional input files are:
CCODE.ins or CCODE.res: SHELXL control data files 
CCODE.cif  : IUCr-ActaCryst CIF data file for crystal data only
 
The crysin file contains the following records:
 
crysin   CCODE    more-info        (header)
TITLE    any user supplied information     (to be printed)
CELL     a b c alpha beta gamma            (Angstrom, degree)
CELLSD   esd's                             (six numbers)
SPGR     e.g. P 1 or P 21 21 21 or R -3    (axial directions are
                                           ( separated by blank(s))
FORMUL   At1 Nr1 At2 Nr2 At3 Nr3 ......    (Ati=chem.symbol,   Nri=nr of
                                           ( atoms Ati ,  max. 10 kinds)
Z        number of FORMUL units / cell
                                      (Note: cell contents = Z * FORMUL)
WAVE     Cu or Mo or Fe or Ag or Cr         (one atom type; no number)
END
 
Notes:
- When during the crystal structure analysis you wish to alter the cell
contents or the space group, you should do this in the crysin file.
 
 

Reflection data files
---------------------
 
Input : <CCODE>.hkl [ priority]  or  fref  

 
CCODE.hkl : SHELX formatted reflection data, 28 characters/record
                         with |Fobs| or |Fobs|**2 values
                         (defined by a HKLF record: default F**2)
 

fref :            formatted reflection data file,   28 characters/record
                               (standard DIRDIF file)  with  Fobs values
      first record:      header with 'fref' or 'frefA' ... and CCODE
      following records: 1 reflection each, FORMAT (A1,3I3,I2,F9.2,F7.2)
                           for:  ' ', h, k, l, '  ', Fobs, sigma 
      last record:       'E'
 
 
orbase and oruser files
-----------------------
 
orbase : a data base with molecular fragments.
oruser : a private extension of orbase  (with your own favourite models)
A write-up of these files is given in the header lines of these files.
The user is urged to add (manually) his own structural molecular
fragments to the file oruser for future use when solving 'similar'
compounds.
 

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