Abstract from: 1-handout.txt [dirdif manual chapter 1]     22 March 2008

A summary about DIRDIF                                       
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          DIRDIF-2008                       A computer program for     
          Crystal Structure Determination by Patterson Methods and
          Direct Methods  applied to  Difference Structure Factors

          How to solve crystal structures using chemical knowledge 
 
          Paul T. Beurskens,   Gezina Beurskens,   Rene de Gelder,      
          Jan M.M. Smits (Nijmegen),   S. Garcia-Granda (Oviedo) &      
                          R.O. Gould (Edinburgh)                       

Notation: all names of programs, parameters, keywords, etcetera, 
    are written in capitals, but all input data may also be given 
    in lower case lettering. All data file names are defined in
    lower case although in write-ups capitals may be used. 

Documents: files stored in directory dirdif/ DOCS  
-  PRIMER files: 1-handout, 2-intro, 3-options, 4.files, 5-monos, etc.
-  gallery.pdf : a visualization of orbase = data base of mol.fragments
-  the MANUAL.pdf : theoretical background of major (sub)programs .

Input data: the usual crystal data and observed reflection data, and
1. ===> for heavy atoms structures: nothing else !
2. ===> for Vector Search: one or MORE known molecular fragments.
3. ===> some options require atomic coordinates.
 
When to use DIRDIF for routine structure analysis:
1.  For structures with heavy atoms, including P and S      call:  PATTY
2.  For structures of molecules with (partly) known geometry ...: ORIENT
 
When to use DIRDIF for (special) problem structures:
3.  For expansion of a small fragment to the complete structure : PHASEX
3.  For an enantiomorph, or a super- or pseudo-symmetry problem : PHASEX

 
How to run DIRDIF  ( CCODE identifies the structure + working directory)
-----------------  [ Change to working directory CCODE ! ]

In most options, the structural parameters ( atomic coordinates,  either
user-supplied  or found by Patterson methods) are expanded  and recycled
(calling repeatedly the appropriate programs) to determine the  complete
structure. Output: atoms file and a copy to CCODE.res .
 
1. Patterson option PATTY for Heavy Atom Patterson interpretation.
   To solve  a heavy-atom  structure  (including S or P  in a light atom
   structure), use PATTY. No input atoms needed. Enter:
=====>   DIRDIF CCODE PATTY
 
2. Patterson option ORIENT for application of Vector Search methods.
   Vector Search methods  are used  when a (relatively small)  part of a
   structure  has known geometry. Prior  to running  ORIENT,  the search
   model  (atmod  file,  fractional  or Cartesian  coordinates)  must be
   prepared.  To verify  the format  of your  prefab  atmod file,  or to
   retrieve a model from orbase  (see ORBASE-GALLERY),  and/or to modify
   the model interactively, enter:
=====>   DIRDIF CCODE ATMOD
   Then, for application of ORIENT (valid atmod file needed), enter:
=====>   DIRDIF CCODE ORIENT
   The orientation of the model is found by program ORIENT, using Vector
   Search. Thereafter, programs TRACOR and TRAVEC are called to position
   the model, and PHASEX and FOUR expand the structure  to completeness.

3. Structure expansion (fractional atomic coordinates in atoms file).
   Expansion and recycling of a partial structure, especially for an 
   enantiomorph, or a super- or pseudo-symmetry problem, enter:
=====> DIRDIF CCODE PHASEX


Adres for correspondence:
     P.T.Beurskens, c/o  Dr. R. de Gelder
     Crystallography Laboratory, Radboud University Nijmegen, 
     Toernooiveld 1,  6525 ED,   Nijmegen,    The Netherlands
     Email: PTBeurskens@hetnet.nl  ( only accepted subject: DIRDIF !)

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