DIRDIF  PRIMER                                             29 March 1997
 
                                  DIRDIF-96
                        a Computer Program System for
           Crystal Structure Determination by Patterson Methods and
           Direct Methods  applied to  Difference Structure Factors
 
       Paul T. Beurskens, Gezina Beurskens, W.P. Bosman, Rene de Gelder,
       S. Garcia Granda,  R.O. Gould,  Randy Israel,  and Jan M.M. Smits
 
             Crystallography Laboratory,  University of Nijmegen,
             Toernooiveld 1,  6525 ED  Nijmegen, The Netherlands.
             FAX: 31-24-3553450            E-mail: ptb@sci.kun.nl
 
Contents                                                            Page
 
Section 1.  Introduction. When to use DIRDIF. Main options & programs  1
Section 2.  How to run the various options of DIRDIF                   4
Section 3.  DIRDIF file definitions                                    8
Section 4.  Examples (test structure MONOS)                           12
Section 5.  How to interpret the results, trouble shooting, restart   14
Section 6.  Notes for various computers                               16
Section 7.  Acknowledgements and references                           18
 
 
 
                                                          Contd:  Page 1
------------------------------------------------------------------------
Section 1.  Introduction.   When to use DIRDIF.  Main options & programs
 

DIRDIF is a composition  of several interrelated computer programs tuned
into a program system for solving crystal structures. Major features are
the use of  Patterson methods,  and special  direct methods  for solving
symmetry problems.  Powerful  procedures  are  provided  for use of your
chemical  knowledge  to solve  difficult  structures.  Ab-initio  direct
methods and least-squares structure refinement  are not included  in the
DIRDIF package.
 
The  program  system  is designed  to operate  under  a wide  variety of
circumstances  using  individual programs and options.  Most options are
fully  automated   according  to  the  black  box  principle,   but  the
(experienced) user has on-line control  for adapting his strategy to the
current problem. An on-line help-facility is provided;  it is limited in
scope and not meant to replace the PRIMER.
 
All programs are written in standard  FORTRAN-77  and are believed to be
as fully  computer-independent  as is  reasonably  feasible.  Inevitable
computer-dependent parts are either provided for common computer systems
or can be bypassed (e.g. the timer routine).
 
When to use DIRDIF for routine structure analysis:
-  For structures with heavy atoms, including P and S ..... call:  PATTY
-  For structures of molecules with (partly) known geometry ..... ORIENT
 
When to use DIRDIF for special problem structures:
-  When ab-initio direct methods gave a misplaced fragment ...... TRACOR
-  For expansion of a small fragment to the complete structure .. PHASEX
-  For enantiomorph or a super- or pseudo-symmetry problems ..... PHASEX
 

Two main pathways in using Patterson methods
 

1.  To solve a heavy atom  structure  (including S or P  in a light atom
structure)  use the program PATTY.  Input:  crystal data and  reflection
data.  No input atoms  or control data needed.  After locating the heavy
atoms the structure is automatically expanded until completeness.
 
2.  To solve a structure with a partly known model  (molecular fragment,
often  a rigid part  of the molecule)  use  Vector Search  methods.  The
search model (file with atomic coordinates) must be prepared in advance.
To retrieve a model  from the ORBASE fragment database  and/or to modify
the model  and/or  verify  the format  of your  prefab file  (all inter-
actively), use the option ORBASE .
      To solve  the structure  with this  search model,  use the program
ORIENT. After orientation,  the model is  automatically  positioned  and
further expanded to the complete structure.
 
 
Main individual programs in the DIRDIF package: a short write-up
 

DDSTART, CRYSDA, MERBIN and DDMAIN  are  programs  which are  essential
members of the system; they are automatically executed when needed, and
they can also be excuted on request of the user, see Section 3. Details
are available also by using the H (=help) options of the system.
 
DDSTART  Starting up  an automatic or interactive run  (including option
         ORBASE)
CRYSDA   Calculation of extended crystal data  (prepare the CRYSDA file)
MERBIN   Prepare a (temporary, binary) reflection data file  (BINFO),  
         Wilson plot, etcetera.
DDMAIN   Various calculations  (Fcalc, R2, etc.)  and recycling control.
 
 
PATTY, ORIENT, TRACOR, PHASEX and FOUR  are  the main  structure-solving
programs. The programs can be called interactively or in automatic mode;
in both cases  the  system will  automatically  continue  to perform all
necessary calculations for the completion of the structure.
 
PATTY    is a program  for the interpretation  of a sharpened Patterson.
         It  uses  Buerger's  implication  theory  (i.e.  the  so called
         symmetry map) and checks all cross vectors  using the  minimum-
         function value as a selection criterion.
        -   The program is used for  heavy atom structures  with unknown
            heavy atom positions (including not-so-heavy-atoms like S or
            P in a light atom structure).
 
ORIENT   is a program  to find  the orientation  of a molecular fragment
         (model) by means of Vector Search methods (Nordman).  The input
         model is used for the calculation  of interatomic vectors.
         The  shape  function  of a single  interatomic  vector  peak is
         approximated from the shape of the origin peak of the Patterson
         function,  and it is used  for the  calculation  of the overlap
         inbetween neighbouring vectors of the model. Vectors to be used
         the search  are selected on weight (including overlap), length,
         and mutual separation.  A fast cyclic  search system in angular
         space (Eulerian angles denoted A, B, C),  employing  increasing
         resolution per cycle,  leads to the best fitting orientation of
         the model.   The fitting  criterion  is  the  Nordman  'minimum
         average' function value.
        -   The program  is used for structures  with known geometry for
            a (relatively small) part  of the molecule.  Note that often
            such a  molecular  fragment  (model)  is available  from the
            user's own collection of related structures.
 
TRACOR   is a program to find the position of a molecular fragment (with
         known  correct  orientation)   by  means  of  reciprocal  space
         correlation  functions.  The input fragment (the ATOMS file) is
         used for the  calculation of  partial structure factors for all
         reflections  (for the entire  expanded  data set).  The partial
         structure factor (which is the sum of partial structure factors
         of symmetry related fragments) depends on the vector t used for
         shifting   the  input  fragment   to   another  position.   The
         correlation between  calculated and  observed structure factors
         (intensities) determines the best value for the shift vector t.
         The calculations are done by the  Fast-Fourier-Transform method
         employing all symmetry elements simultaneously.
        -   The program  is used  for positioning a  structural fragment
            with correct orientation  but unknown position.  The program
            is  automatically  executed  in the procedure  initiated  by
            calling ORIENT (see above).
        -   A correctly oriented fragment  sometimes is available as the
            result of a failure of ab-initio direct methods;
            when a recognizable  fragment  does not allow  expansion  or
            refinement,  then the fragment may be misplaced,  though the
            orientation is correct.
 
PHASEX   is a program to EXpand and refine the PHASes  of the difference
         structure  factors  by  direct methods.  The input fragment  (a
         correct  but incomplete set of atomic parameters,  for instance
         known  heavy  atoms  or  an oriented  and positioned  molecular
         model)  is used  to calculate  normalized  difference structure
         factors (Wilson-Parthasarathy) giving 'E1' values.  Weights are
         calculated (Woolfson or Sim)  and the  E1 values  with the most
         reliable  phases are  input to a  modified  tangent  formula to
         refine  the input phases and  to calculate  phases for unphased
         reflections.
    The application of DIRect methods to the DIFference structure
    factors is particularly powerful:
    .    when the known part of the structure is only marginally
         sufficient to solve the structure,
    .    when the model has higher translation symmetry than the space
         group (superstructure),
    .    when the centrosymmetric input model comprizes an enantiomorph
         problem,
    .    when the known atoms comprise another pseudosymmetry problem
         such as a 'chicken wire' fragment.
    The program recognizes the symmetry problem and uses a special
    symbolic addition procedure to solve the enantiomorph and/or
    origin ambiguity problem.
        -   The program is used for expanding a partial structure. The
            program is automatically executed in the procedures
            initiated by calling PATTY, ORIENT or TRACOR.
 
FOUR     is a program for the calculation of Fourier and Patterson maps.
         It implies calculation of distances and angles,  assignment and
         shuffling  of  new  peaks  into  connected  atoms,  plotting of
         the asymmetric part  of the structure.  The program  FOUR  also
         arranges for  further expansion of the structure  and recycling
         (reactivating programs DDMAIN, PHASEX and FOUR).
         Note that the  program's  decision of  how to assign peaks  and
         which atoms to use  is based  on peak  heights and  geometrical
         considerations, but not on valid  chemical arguments:  the user
         should apply  his chemical knowledge  and make  the appropriate
         modifications in the final output atomic parameters.
        -   The program uses  input files  generated by  other  programs
            (via program DDMAIN).  It is  automatically  executed in the
            procedures  initiated  by calling  PATTY, ORIENT, TRACOR  or
            PHASEX.  When the known part  of the structure is relatively
            large,  program FOUR is executed  instead of  PHASEX because
            the difference structure factors then are unreliable.
 
Finally we describe  the two options  ORBASE  and  DIRP1,  the parameter
NORECY, and two more programs: TRAVEC and NUTS.
 
ORBASE   is a special  option  which can be used  to prepare  a suitable
         model for input to the  Vector Search program  ORIENT.  A model
         can  be  selected  interactively  from  the  ORBASE  or  ORUSER
         database of  molecular fragments.  (See  ORBASE-GALLERY.)  Some
         facilities are available for modifying the model.
 
DIRP1    is  an  option  that  can  be  useful  for  the solution  of  a
         structure  in case the user is uncertain about the space group,
         the composition of the compound,  and/or  the position  of some
         heavy atoms.  The option DIRP1 causes the reflection data to be
         expanded  to space group  P1  (or  centered equivalent e.g. C1)
         and calls  the option  PHASEX  for elucidation of the structure
         in P1.  The input model may be, for instance, one heavy atom in
         the origin!
 
NORECY   is an  additional calling parameter  which is used  to suppress
         the automatic recycling procedure.  The keyword NORECY is added
         to the  calling parameters.  The recycling  should be  bypassed
         only when the automatic procedure failed to solve the
         structure.
 
TRAVEC   is  a  program  which  is  automatically  executed  after   the
         execution of TRACOR:  it is based on vector search methods, and
         it calculates a FOM (figure of merit) which helps to select the
         best shift vector t from the TRACOR results:  in a few cases an
         erroneous TRACOR result is corrected by TRAVEC.
 
NUTS     is a collection of sub-programs for various  utility functions:
     AT2X     conversion of ATOMS to XYZN (for SHELXL) and other formats
     X2AT     conversion of XYZN to ATOMS (DIRDIF format)
     BIJVOET  calculation of absolute configuration
     SHAT     shift atoms
     EULER    rotation of a rigid fragment  (by A,B,C, in angular space)
     INVERT   inversion of atomic parameters
 
 
 
                                                          Contd:  Page 4
------------------------------------------------------------------------
Section 2.     How to run the various options of DIRDIF
 

Preliminary comments on input/output files (for more information, see
Section 3.)
      Most programs need a reflection data file and a crystal data file.
For the application of vector search methods (ORIENT), the user has to
prepare the ATMOD file (with the a-priori known molecular geometry)
either before the automatic execution of ORIENT, or in an interactive
session on request. In some cases (problem structures) the user has to
prepare an ATOMS file.  No control data is needed.
      Atomic parameters of all possible solutions obtained by programs
PATTY or ORIENT and TRACOR, and also atomic parameters of some
intermediate results (program FOUR) are stored in the ATOLD file (back-
up). The DDLOG file keeps record of some data of subsequent runs.
      When the structure has been solved you find results and comments
on the LIS1 and LIS2 files and the atomic parameters of the structure
on the ATOMS file as well as on an XYZN file  (equivalent to SHELXL's
INS file).
 

Instruction syntax
------------------
CCODE: compound code,   PROGRAM: program name or option,    ====> :enter
 
For the execution of any of the structure-solving programs PATTY,
ORIENT, TRACOR, PHASEX, and FOUR the user has the choice between the
automatic mode and the interactive mode:
=====>   DIRDIF  CCODE  PROGRAM          for automatic execution
=====>   DIRDIF  CCODE                   for interactive execution
In the interactive mode every question is provided with a help facility.
 
The execution of CRYSDA, MERBIN, NUTS and any of the programs collected
in NUTS (AT2X, BIJVOET, etc., see Section 1) is interactive:
=====>   DIRDIF  CCODE  PROGRAM
=====>   DIRDIF  CCODE
 
 
Patterson  path I : run PATTY for Heavy Atom Patterson interpretation.
------------------------------------------------------------------------
When the structure contains Heavy Atoms (including S or P in a light
atom structure):
 
=====>   DIRDIF CCODE PATTY
      No input atoms needed. The system automatically arranges for the
      following procedure: first calculate the Patterson function
      (program FOUR), then locates the heavy atom(s) (program PATTY),
      expand the partial structure (program PHASEX, followed by FOUR),
      and recycle several times (programs DDMAIN, PHASEX and FOUR) for
      complete elucidation of the structure. Output: structural
      parameters in the ATOMS file.
 
 
Patterson  path II: run ORIENT for application of Vector Search methods.
------------------------------------------------------------------------
Vector Search methods are used when a (relatively small) part of a
structure has known geometry. The known part usually (but not
necessarily) is a rigid molecular fragment. The search model (ATMOD
file, fractional or Cartesian coordinates) must be prepared before
executing ORTIENT (see Section 3 for the write-up of the ATMOD file):
 
=====>   DIRDIF CCODE ORBASE
      Procedures:
   a:    When the user has prepared an ATMOD file in advance (from
         literature data, molecular modelling or his own archieves):
         checking the format of the file.
   b:    Else: interactive retrieval of a model from the database ORBASE
         and/or ORUSER (see the fragments listed in the ORBASE-GALLERY).
   c:    In either case: interactive fragment modification (add atoms,
         delete or rename atoms, etcetera).
      Output: an (updated) ATMOD file with Cartesian coordinates.
 
=====>   DIRDIF CCODE ORIENT
      To apply Vector Search methods in automatic mode. Input: ATMOD
      file.
   -  When the user calls for ORIENT, the system automatically arranges
      for the following procedure: first check and perhaps rewrite the
      ATMOD file with the atomic parameters of the model, then calculate
      the Patterson function (program FOUR), search for the orientation
      of the model (program ORIENT), use translation functions to
      position the model according to space group symmetry (program
      TRACOR followed by TRAVEC, see below), expand the partial
      structure, and recycle several times (programs DDMAIN, PHASEX,
      FOUR) for complete structure elucidation. Output: ATOMS file with
      final atomic parameters.
 

Additional options  (for various kinds of problems)
------------------

=====>   DIRDIF CCODE TRACOR
      Input fractional atomic coordinates given in an ATOMS file.
   -  The program is used for expanding structural fragments with cor-
      rect orientation but unknown position. The program is automatic-
      ally executed in the procedure initiated by calling ORIENT.
   -  The program is explicitely called by the user in a number of cases
      a.  If the 'best' solution from the vector search procedure
      (ORIENT) failed to solve the structure, the user may supply the
      'second best' solution of ORIENT (available in the back-up file
      ATOLD, to be copied to ATOMS file), and call for TRACOR.
      b.  In enantiomeric space groups an asymmetric model (correctly
      oriented by ORIENT) may have to be inverted  (program NUTS INVERT)
      before calling TRACOR again.
      c.  A correctly oriented fragment sometimes is available as the
      result of a failure of ab-initio direct methods; when a recogni-
      zable fragment does not allow expansion or refinement, then the
      fragment may be misplaced, though the orientation is correct. The
      user may supply this fragment (input: ATOMS file) and call for
      TRACOR.
      d.  The program is also a powerful tool for the elucidation of
      heavy atom structures. For instance, the origin and the next
      largest non-Harker Patterson peak define a pair of heavy atoms
      which can be used as a well oriented model to be positioned by the
      program TRACOR.
   -  When the user calls for TRACOR, the system automatically arranges
      for the following procedure: first expand the reflection data to
      a half-sphere and use the fragment to calculate partial structure
      factors (program DDMAIN), then find the position of the fragment
      (programs TRACOR and TRAVEC), expand the partial structure and
      recycle (programs DDMAIN, PHASEX and FOUR) to complete the
      structure elucidation. Output: ATOMS file with atomic parameters.
   -  (Note: the user cannot call program TRAVEC individually.)
 
=====>   DIRDIF CCODE PHASEX
      Expansion and recycling of a partial structure, i.e. when some
      atoms are known (on correct positions). Input fractional atomic
      coordinates are given in the ATOMS file.
   -  The program is automatically executed after PATTY, ORIENT or
      TRACOR.
   -  The program is explicitely called by the user in a number of cases
      a. If the 'best' solution from either PATTY or TRACOR failed to
      solve the structure, the user may supply the 'second best'
      solution (available in back-up file ATOLD, to be copied to ATOMS
      file), and call for PHASEX.
      b. The user should call for PHASEX when he has his own suggestions
      for atomic positions: for instance he may have modified the atoms
      in the ATOMS file available from a foregoing DIRDIF run (which, of
      course, is only useful if something went wrong ...).
   -  When the user calls for PHASEX, the system automatically arranges
      for structure factor calculation and normalization (program
      DDMAIN), then executes the program PHASEX to expand and refine the
      phases of the difference structure factors, calculates and
      interprets a Fourier synthesis (program FOUR), and finally organi-
      zes recycling several times (programs DDMAIN, PHASEX and FOUR) for
      expansion of the fragment and completion of the structure. Output
      atomic parameters in ATOMS file.
 
=====>   DIRDIF CCODE FOUR
      The program FOUR is automatically executed after PATTY, ORIENT,
      TRACOR or PHASEX
   -  The program is explicitely called by the user in a number of cases
      similar as for PHASEX (see above). Input: ATOMS file.
   -  When the user calls for FOUR, the system will automatically
      arrange for structure  factor calculation (by program DDMAIN)  and
      then  calls  program  FOUR  for a default  Fourier synthesis.  The
      program FOUR then  arranges  for recycling  (programs  DDMAIN  and
      FOUR)  until the structure evaluation  is completed.  Intermediate
      atomic parameters are saved in the ATOLD file, final output atomic
      parameters in the ATOMS file.
 
=====>   DIRDIF CCODE NUTS    (or for instance  ===> DIRDIF CCODE AT2X )
      This call invokes an interactive session for the execution of
      various utility calculations. One option is AT2X, a subprogram for
      the conversion of the final ATOMS file into files for other
      propgrams (SHELXL, PLUTON, SCHAKAL). Other options (sub-programs)
      are X2AT, BIJVOET, SHAT, EULER, INVERT: call NUTS for more
      information.
   -  The program NUTS (option AT2X) is automatically executed in all
      structure solving procedures after the final execution of program
      FOUR.
 
=====>   DIRDIF CCODE CRYSDA
      To prepare the CRYSDA file.  Usually the call for the program
      CRYSDA is invoked automatically.
   -  When the user wishes to modify the crystal data, he should first
      of all erase the CRYSDA file, then modify the CRYSIN file.
 
=====>   DIRDIF CCODE MERBIN
      To prepare the BINFO file.
      Usually the call for MERBIN is invoked automatically.


In case of problems:
 
=====>   DIRDIF H
      Invokes a short help session. (No CCODE given, no data needed.)
      For the new DIRDIF user it is really useful to try out all
      possibilities in order to get used to the system.
 
=====>   DIRDIF CCODE
      Starts an interactive run.
   -  When DIRDIF is activated in interactive mode the user is asked to
      select an option or program (ORIENT, PATTY,...) and then whether
      or not special control data is wanted. Interactive help facilities
      are available. For a first run we strongly advise to use the
      default values.
 
=====>   DIRDIF CCODE DIRP1
      Starts a procedure which helps the user to solve the structure in
      P1.
   -  It is used in case the space group, the composition of the
      compound, and/or the position of some heavy atoms are very
      uncertain. The input partial structure (ATOMS file) may be, for
      instance, one atom in the origin!
   -  Procedure: the reflection data are expanded to space group P1 (or
      centered equivalent e.g. C1) and the program PHASEX is executed
      for elucidation of the structure in P1. (The one-atom case is made
      asymmetric by the enantiomorph-fixing procedure.)
   -  After inspection of the results the user decides how to continue.
      There is no automatic recycling. After several 'hand'-controlled
      restarts (editing the output ATOMS file by hand, perhaps changing
      the crystal data), the user must recognize and locate the symmetry
      elements himself.
 
=====>   DIRDIF CCODE PHASEX NORECY
      Starts an automatic PHASEX run, but suppresses the recycling
      procedure !
      (Similar for options  PATTY, ORIENT and TRACOR).
 

Restarting DIRDIF
------------------

When you want to rerun one of the options of DIRDIF you have to consider
which atomic parameter set is to be used as input. You can start your
own recycling procedure using the existing ATOMS file (output from last
DIRDIF run), or you can select one of the parameter sets stored in the
back-up file ATOLD and copy it to the ATOMS file. Use local editing
facilities to modify the ATOMS file to suit your idea of the best set of
atomic parameters.
To decide which option of DIRDIF you want to call, consider their
consecutive actions:
 
         find heavy   fragment       fragment      fragment       make
         atom(s)     orientation    positioning   expansion*    Fourier*
call:
PATTY    PATTY  --------------------------------->  PHASEX  ----->  FOUR
ORIENT                ORIENT ----->  TRACOR ----->  PHASEX  ----->  FOUR
TRACOR                               TRACOR ----->  PHASEX  ----->  FOUR
PHASEX                                              PHASEX  ----->  FOUR
FOUR                                                                FOUR
 
* PHASEX and/or FOUR are recycled by default until completion of the
structure. The recycling procedure is suppressed by the calling
parameter 'NORECY'.
 
 
                                                                  Page 8
------------------------------------------------------------------------
Section 3.     DIRDIF file definitions
 

Filenames are dependent on the computer and on local use.  The different
files of the DIRDIF system  are referred to by its functional type.  The
filename dictates the contents  and the format of the file !  Within the
FORTRAN programs  and in all documents  (also in this PRIMER), filenames
are represented by capital letters.  They may locally  be transcribed to
lower case,  and maybe  concatenated by  compound code or directory name
(or otherwise changed to local conventions).
Example: for the test compound MONOS the primary crystal data is given
in the CRYSIN file. For the PC-version of DIRDIF the filename remains
CRYSIN. For the VAX-VMS version the filename is CRYSIN.DAT . For all
unix systems the same file is called monos.crysin . Etcetera.
 
Standard file structure:  Most files consist of free-format records of
at most 72 characters each. The order of words (literals, numbers) in a
record is fixed. The first word of a record is a keyword for
identification. The first record usually is a header record with at
least FILENAME and CCODE. REMARK records (keyword=REMARK) (with
printable information) may be inserted anywhere. The last record is an
END or a FINISH record.
Note: reflection files have fixed format; REMARK records are not
permitted.
 
DIRDIF needs an input reflection data file. The primary crystal data may
be supplied manually, but it is preferred  to prepare the CRYSIN file in
advance. For some options atomic parameters files are needed  (the model
parameters given in  file ATMOD,  or parameters of the partial structure
given in file ATOMS).   Other files are output files. 

 
3a.   Listing files LIS1 and LIS2
---------------------------------

The system produces a file for printing (LIS1 = printable output) which
gives the most important information on the solution of the structure.
In addition a longer listing file, LIS2, is produced which gives
information on the input data, the execution of the various programs,
and their results. Inspect the file LIS2 only if you are interested or
when the structure did not come out as you hoped or expected. With the
aid of the detailed information you might be able to detect where things
went wrong, then change input data and start DIRDIF again. Certainly
LIS2 should not be printed routinely. But if things really go wrong, do
send the LIS1 and LIS2 prints (files) to Nijmegen: we will be glad to
help you!             Note: the LIS-files are overwritten in a next run.
 
 
3b.   Atomic parameter files ATOMS and ATMOD
--------------------------------------------

The input and output atomic parameter files of the DIRDIF system are:
- ATOMS file: input to most programs, overwritten with output
parameters,
- ATMOD file with the model parameters input to the program ORIENT,
- ATOLD file: a collection of parameter sets, to be used as back-up
file,
- XYZN, SPF, SCHAKAL: for communication with other program systems.
      (For instance: when XYZN is renamed to INS, the file is ready for
      input to the SHELXL least-squares refinement program.)
 
The ATOMS file consists of the following records, each containing a
keyword followed by data:
 
ATOMS    CCODE    more-info       (header record. CCODE = compound code)
ATOM     atomname   x  y  z       (x,y,z: fractional atomic coordinates)
                                  (one atom / record, as many as needed)
REMARK   comments                 (optional,  anywhere after the header)
END                               (last record)
 
The atomname begins with the chemical symbol and may be followed by one
or more characters (e.g. C7, C+7, C7+, C7A are carbon atoms; CA is a
calcium atom, CX is an error). Alternatively the atomname may consist of
the chemical symbol, one or more blanks, and one unsigned integer number
( e.g. C  27 ). Uninterpreted (residual) peaks of a Fourier map are
given atomname = Q .
 
It is possible to supply a site occupancy factor sof (sof = 1.00 also
for atoms on special positions; sof < 1.00 for disordered atoms) and an
isotropic temperature factor (B) on the ATOM record, but do so only if
you are sure about the data, because it will have a significant effect
on the scaling procedure.
 
When the structure has been solved the output ATOM records are provided
with 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 NUTS/AT2X converts
the output ATOMS file to an XYZN file (equivalent to the INS/RES files
of the least-squares refinement program SHELXL) and (optional) to SPF
and SCHAKAL files (input to graphics programs PLUTON and SCHAKAL,
respectively).
 
 
The ATMOD file has the same structure as the ATOMS file.
--------------
               The first record is the header record.
               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)
               The records with with atomic parameters (one atom/record,
               as many records as needed) contain either fractional 
               coordinates or Cartesian coordinates:           
ATOM     atomname    x  y  z               (fractional coordinates)
ATOM     atomname    X  Y  Z               (Cartesian  coordinates)
                                   For the atomname see under ATOMS file                                                                                                                                                                                                                                                                                                                                                                                                                                                        
REMARK   comment                   (optional, anywhere after the header)
END                                        (last record)
 
Notes.
The information CART (for Cartesian) is optional as DIRDIF finds out
whether the parameters are fractional or Cartesian. The information
'MCELL a b c alpha beta gamma' is necessary only when the fractional
atomic parameters of the model or fragment are represented in a unit
cell that is different from the present compound CCODE.  (Instead of
'MCELL' also 'CELL' is accepted.) In an interactive session the MCELL
data can also be provided at the terminal.
 
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.
 
The ATMOD file, described so far, is input (e.g. by instruction: DIRDIF
CCODE ORBASE), and after checking, editing, and possible re-orientation,
a new ATMOD file is output with Cartesian coordinates (the original
input file is saved in the ATOLD file for back-up).
 

3c.   Crystal data files
------------------------

CRYSIN :       primary crystal data: standard DIRDIF input file
INS or RES :   SHELXL control data file (see SHELXL write-up)
CIF :          IUCr-ActaCryst. CIF file for crystal data only 
CRYSDA :       extended crystal data, generated by the program CRYSDA


At a first run for a given CCODE, when the CRYSDA file does not exist,
the program CRYSDA (usually called automatically) reads crystal data
from a CRYSIN file (highest priority) and/or from other input
possibilities (INS/RES, CIF, keyboard) and produces a CRYSDA file which 
contains the input crystal data and extended data such as cell volume, 
calculated density, tables of scattering factors, etc.
If the primary crystal data is incomplete, DIRDIF will ask for the
missing items.
If no CRYSIN file was available, or if the data in the CRYSIN file was
incomplete, or if the crystal data was modified interactively, a (new)
CRYSIN file will be output. Normally the CRYSIN file is to be kept.
 
 
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)
         At7 Nr7 At8 Nr8 At9 Nr9 ......    (continuation record allowed)
                                           Example:    for  Na2CO3.7H2O:
                                           FORMUL NA 2 C 1 O 3  H 14 O 7
Z        number of FORMUL units / cell
                                      (Note: cell contents = Z * FORMUL)
                                        (! Z is not a symmetry factor !)
WAVE     Cu or Mo or Fe or Ag or Cr         (one atom type; no number)
ORIN     crystal orientation matrix         (OPTIONAL,  3 records)
END
 
Note:  When during the crystal structure analysis  you wish to alter the 
cell contents or the space group, you must delete the CRYSDA file and
then modify the CRYSIN file !
 
 
3d.   Reflection data files
---------------------------

Input (formatted):   FREF  alias  FREFA  FREFB  FREFC  (standard DIRDIF)
or input (formatted): HKL  alias  SHELX  SHELXL (SHELXL reflection file)
Output (binary):     BINFO (temporary file, generated by program MERBIN)
 
The program MERBIN  (usually called automatically)  
finds out which data file is present, it reads the reflection data, 
and writes a temporary binary reflection data file BINFO. 
Formats of the reflecton data files:
 

FREF alias FREFA FREFB FREFC: 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, JC, Fobs, sigma
                              JC=2 for 'unobserved' or 'unreliable',
                              else JC=1 or blank
      last record:       'E'
 
 
HKL alias SHELX SHELXL:  formatted reflection data file,
-----------------------  28 or more characters/record
                         with either Fobs or (Fobs)**2 values
      First record:      HKLF record (optional!, not SHELXL convention!)
                         (see NOTE)
                  First word:      'HKLF' on columns 1 - 4
                  Second word:     CCODE   (optional)
                  and one number:  3 or -3 : Fobs expected or
                          or:      4 or -4 : (Fobs)**2 expected !
      Following records: 1 reflection/record,  SHELXL format:
                  FORMAT (3I4, 2F8.2) for:  h, k, l, Fobs, sigma
                                      or:   h, k, l, (Fobs)**2, sigma
                (Note: the SHELXL batch number on cc. 29-32 is ignored.)
      Last record:       h = k = l = 0 (or: all blanks)
 

NOTE: The presence of Fobs or (Fobs)**2 on the HKL file is defined by
      the HKLF record given in the INS file (instructions for SHELXL) or
      as the header of the HKL file (for DIRDIF only). If the HKLF 
      record is not available, then the program MERBIN will ask whether 
      F's or squared-F-values are present on the HKL file. 
      There is no default.
 
      (Note about the SHELXL indices transformation matrix  Rij given on
      the HKLF record of the INS file: This feature
      should be used with care !! It is not used on crystal data!)
 
Mind that a CIF file or an INS/RES file (SHELXL) can only be used
directly as an input file for the program CRYSDA. The CIF and INS/RES
files can not be used as reflection data input files.
 
 
3e.   DDLOG file ('readable data')
-----------------

This file contains a summary of DIRDIF runs with pertinent data. This
file is to be kept.
 
 
3f.   ORBASE and ORUSER files
-----------------------------

ORBASE : a data base with molecular fragments 
         (format: concatenated ATMOD files).
ORUSER : a private extension of ORBASE  (with your own favourite models)
         (same format)
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 frag-
ments in the file ORUSER for future use when solving similar compounds.  
 

                                                                 Page 12
------------------------------------------------------------------------
Section 4.     Examples (structure MONOS)
 

You may wish to get acquainted with DIRDIF by running an example. We
have provided the data for the test structure MONOS.
 

Preliminaries
 
- Run the DIRDIF system for help.
      The help facility can be used without the presence of the data of
      the test structure. Enter at the terminal: ====> DIRDIF H
      You will be given some information. Please, try out all
      possibilities, in order to learn about various conventions and
      options.
- Look at the MONOS data files (change directory to MONOS ?).
      The crystal data for MONOS are given in the CRYSIN file.
      The molecule contains a sulfur-bridged six-membered ring which is
      given in ORBASE under the model name MONOS.
- What to do if more MONOS data files are present (e.g. from former test
  runs)?
      You do not have to erase any file unless there was a computer or
      program crash. If you wish to have a 'cold' start with MONOS:
      erase at least the CRYSDA and DDLOG files.
 
Proceed to run DIRDIF with the data of test structure MONOS, solving the
structure of MONOS along three different routes, depending on the a
priori information you assume to know:
route 1:  call program PATTY,  using DIRDIF in automatic mode   (RUN 1),
route 2:  call program PHASEX, using DIRDIF in automatic mode   (RUN 2),
route 3:  call ORBASE (interactive mode) and ORIENT automatic (RUN 3+4).
 
 
RUN 1.   Route 1: option PATTY in automatic mode
------------------------------------------------
 
We know there is a sulfur atom, but we assume not to know its position.
We start an automatic (default) run of DIRDIF program PATTY. The
following files are input:
CRYSIN   crystal data
FREF     reflection data file
 
Enter at the terminal:
=====>   DIRDIF MONOS PATTY
 
The program PATTY finds the sulphur atom at a pseudo-special position.
To handle this problem the program PHASEX runs through an enantiomorph
fixing procedure. The course of the recycling procedure can be followed
on the screen. When the program has finished the structure has been
solved. The LIS1 file gives the most interesting features of the
procedure and a line-plot of the structure. The ATOMS file contains the
parameters of the atoms of the structure. It appears that all atoms are
correctly nominated (S, O, N, C).
 
The following files have been created (look at these files using your
local editor):
CRYSDA   expanded crystal data
ATOLD    atomic parameters of consecutive steps in the procedure
ATOMS    atomic parameters of the complete structure
XYZN     converted ATOMS file to SHELXL format
DDLOG    information on this run and some important data
LIS1        file for printing
LIS2     (ignore, use only in case of problems)
 
When DIRDIF is used again on MONOS  (and you did not erase the CRYSDA
file)  it bypasses the generation of the CRYSDA file file.    
The information on the ATOLD file and on the DDLOG file will be extended
in following runs of DIRDIF. The files ATOMS, XYZN, LIS1 and LIS2 files
are overwritten in a next run. So, do not delete the files that have
been created by this run before you run RUN 2.
 
 
RUN 2.   Route 2: option PHASEX in automatic mode

-------------------------------------------------
Assume for test RUN 2 that we know the position of the sulfur atom. To
put in the position of the sulphur atom you modify the file ATOMS which
has been created in RUN 1 so that it contains the atomic parameters of
the sulphur atom only. So make the ATOMS file to contain:
ATOMS    MONOS
ATOM     S  -0.020 0.098 0.146
END
 
The following files now are available for input:
ATOMS    this file was just prepared manually
CRYSDA   this file has been generated in RUN 1
FREFA    this file has been unchanged

We start an automatic (default) run of DIRDIF program PHASEX.
Enter at the terminal:
=====>   DIRDIF MONOS PHASEX
 
The sulphur position on x = -0.020 does not have the pseudo-symmetry
which occurred in RUN 1, so PHASEX does not run through the enantiomorph
fixation. (Note: x=+0.02 gives the enantiomer!)  When the program has
finished the structure has been solved, the LIS1 file shows the
structure, and the ATOMS file contains the parameters of the atoms of
the structure. The final results are almost identical to the outcome of
RUN 1. (Note: one can not predict whether PATTY finds a positive or a
negative x value for the sulphur position).
 
The following files have been overwritten  (look at these files using 
your local editor):
ATOMS    atomic parameters of the complete structure
XYZN     converted ATOMS file to SHELXL format
LIS1     file for printing
LIS2     (ignore, use only in case of problems)
 
New results have been appended to the following files:
ATOLD    atomic parameters of consecutive steps in the procedure
DDLOG    information on this run and some important data
 
 
RUN 3+4.   Route 3: option ORIENT in interactive mode
-----------------------------------------------------

Assume that we know a rigid fragment of the structure, which is
available in the ORBASE file.  We start (RUN 3)  with calling ORBASE for
an interactive retrieval of  the rigid fragment from ORBASE  as a set of
atomic parameters (7 atoms) which will be stored in file ATMOD. 
Next (RUN 4) we call an automatic run o ORIENT.
 
The following files are available for input:
CRYSDA   this file has been generated in RUN 1
FREFA    this file has been unchanged


For RUN 3, enter at the terminal:
=====>   DIRDIF MONOS ORBASE
 
In the following dialog you may also answer in lower case.
                                                         | You answer at
On the screen appears:                                   | the terminal:
                                                       
- Please give TITLE                                             | Test 3
- No ATMOD file. Can you supply the atomic parameters           |
      now at the termonal (T) or did you Select or do you       |
      Suggest an item from ORBASE (S)                           | S
- Enter model code or number                                    | MONOS
                   (if necessary:  clear screen and hit         : enter
- Schematic picture of the model. Just let us try some things.. |
      Enter first letter of Edit option                         | X 10
      Enter first letter of Edit option                         | X 80
      Enter first letter of Edit option                         | G S1
      Enter first letter of Edit option                         | Q
- Is this result acceptable? (Y/....)                           | Y
 
The following file will be cretaed
         (look at this file using your local editor):
ATMOD    atomic parameters of the model in Cartesian coordinates


For RUN 4, enter at the terminal:
=====>   DIRDIF MONOS ORIENT
 
The program ORIENT reads the model and rotates it, the program TRACOR
shifts it to the correct position (verified by TRAVEC) and the program
PHASEX expands the model to the complete structure. When the recycling
procedure is finished, the structure is solved. The LIS1 file shows some
intermediate results and a line-plot of the structure. The output ATOMS
file contains the parameters of the atoms of the structure. It appears
that within the original input fragment the two nitrogen atoms are
placed at carbon positions, and v.v. (Note: the N-C interchange is the
result of the ORIENT output; one of the other acceptable orientations of
the input model does not have this interchange.)
 
The following files have been updated
         (look at these files using your local editor):
ATOLD    atomic parameters sets of various steps in this run (and in
         former runs)
ATMOD    atomic parameters of the model in Cartesian coordinates
         (unchanged after RUN 3A)
ATOMS    atomic parameters of the complete structure
XYZN     converted ATOMS file to SHELXL format
DDLOG    information and data on this and preceding runs
LIS1     file for printing
LIS2     (ignore, use only in case of problems)
 
 
                                                          Contd: Page 14
------------------------------------------------------------------------
Section 5.     How to interpret the results,
               trouble shooting, how to restart
 

How to interpret the results
 
Use your own graphics and your chemical knowledge to edit the final
parameters (maybe delete or rename some atoms). The table of bond
distances and angles printed in LIS1 will be of help. lf necessary, 
restart DIRDIF to find some more atoms. The final XYZN file, 
renamed to INS, is ready for use by the program SHELXL.
 

Trouble shooting
----------------

1.    The best way to learn about DIRDIF is to use it as a routine tool
      for solving crystal structures. Although DIRDIF is designed for
      delivering automatically the complete set of atomic positions, it
      is useful to read some of the output listings (LIS1) in order to
      learn about the way things are done for normal (routine)
      structures.
 
2.    In this section we will give some comments and suggestions which
      may be useful in special cases. Naturally these are ad-hoc type
      notes: suggestions given here may be obsolete after next program
      updates.
 
3.    If you have enough experience with the automatic runs, it is time
      to try out the various options in interactive mode (with user
      intervention) and to supply different control data to rerun some
      of the structures you have solved earlier. Note: you may answer
      'H' to all questions to get (some) help-information.
 
4.    The programs ORIENT, TRACOR, and PATTY usually lead to more than
      one acceptable solution, and the best solution is automatically
      accepted for further elucidation of the structure. If the
      structure is not solved this way, one should take the second (and
      maybe the third, ...) solution (stored in the ATOLD file), put it
      in the ATOMS file, and call for the appropriate program (TRACOR
      for the second ORIENT solution, etc.).
         NOTE: look at the relative peakheights (figures of merit) for
      various possible solutions in PATTY, ORIENT and TRACOR: you will
      soon get some experience in judging whether or not a "second"
      solution may be the correct solution!

5.    If you are going to restart DIRDIF using a parameter set taken
      from ATOLD, or if you are modifying the existing ATOMS file, it
      is strongly advised to remove the individual B values from the 
      ATOM records. Similarly:
 
6.    DIRDIF usually uses scale and temperature factors from previous
      runs. A former incorrect set of atomic positions may have resulted
      in bad scaling procedures. A fresh start can be obtained by
      deleting all individual B's from atoms that you have selected 
      (in the ATOMS file) for recycling.
 
7.    The 'NORECY' option is used in case you hope to find a chemically
      reasonable fragment from a Fourier peak list in those troublesome
      cases where the automatic recycling failed. In this case, however,
      the R2 criterion is not used for rejecting atoms.
 
8.    A failure of the computer or a technical error in our programs may
      lead to a supervisor-interrupt, in which case the system may stop
      without properly deleting or closing various files. This may cause
      severe problems at the next run! Simply erase all files which are
      unknown to you, just be careful not to delete your primary data
      files or the back-up ATOLD file!
 
9.    In case of a technical program failure, please give us the
      details: we wish to correct the programs.
      In case the DIRDIF system cannot solve your structure, please let
      us know: maybe we can help, most probably we can learn from it.
 
10.   About ORIENT: a very small fragment, especially a simple 5- or 6-
      membered ring, fits almost everywhere in the Patterson. Try to
      find  a bigger fragment with more characteristic geometry, even at
      the cost of accuracy of the model.
 
11.   Reading messages and looking at numbers in the output LIS1 file ?
      -  If an uninterpretable error message occurs, write to us: we
         know and can tell you.
      -  Look for error messages or possible 'WARNINGS'.
      -  Are the temperature factors normal ?
      -  Are high-order reflections adequately measured (not too many
         unobs)?
      -  Look at the Patterson peaks: is all O.K. ? No apparent space
         group error?
      -  See if (for ORIENT) the Patterson origin peak is about zero.
      -  See if (in PHASEX) the evarage E**2 converges to about 1.00
      -  .... and the tangent-refinement-consistency decreases to < 0.50
      -  .... the number of participating reflections is 'normal' ...
      -  Is the actual R2 decreasing during the R2-controled recycling ?
      -  How is the distribution of peaks in the final Fourier map? Too
         many clusters?
      By looking at those numbers and messages after the structure
      solution of normal structures, one knows what to expect, and one
      can often find clues in the output LIS1 file for failures or
      problems encountered with 'difficult' structures. (The output
      listing file LIS2 also might give information.)
 

Restarting DIRDIF
------------------

If your structure does not come out as you wish or expect, and you have
detected where the solution of the structure (probably) went wrong, you
can rerun part of DIRDIF either with non-default parameters, or with a
changed model, or using the second solution of ORIENT or TRACOR, etc.
Several suggestions are given in section 2.
 
After several cycles, the recycling strategy tends to limit the number
of atoms which may be rejected by the R2 criterion. When the recycling-
procedure is very slow (or the actual R2 decreases too slow), it is
usually caused by the presence of too many erroneous peaks in a light-
atom partial structure, or by false assignment of one or more heavy
atoms. Do restart PHASEX after rejection of the majority of the atoms
and perhaps renaming some of the heavy atoms. Let the peakheights be
your guide! This way the recycling procedure gets a fresh start and
PHASEX is most powerful for small fragments!

Sometimes DIRP1 is an interesting option (especially if many things are
uncertain). It requires that the user selects his own set of atoms, and
(when nesessary) updates the cell contents in the CRYSIN file, and
interactively modifies the scale factor and the temperature factors. As
early as possible he must find possible positions of the symmetry
elements, and select atoms in such a way that the superfluous artificial
symmetry is reduced. Experimental TRACOR runs may help to locate the
symmetry elements. The set of atoms may be shifted using the program
NUTS.
 
Note: it is easy to solve a space group uncertainty by restarting DIRDIF
using different space groups (delete the CRYSDA file and modify the
space group in the CRYSIN file !).
 

 
                                                          Contd: Page 16
------------------------------------------------------------------------
Section 6.     Notes for various computers
 

Technical details are given in the various IMPLEM and EXEC files. The
notes given here are related to practical use of DIRDIF and are based
upon distributed implementation instructions. (Private implementations
are easily made: instructions are given in the various distributed NIJX*
files.)
 

Directories and filenames for PC and VAX computers
 
When you start working on a new compound you must first create a
directory, probably named after your compound code CCODE, in which all
files relating to this compound are (will be) stored (see the imple-
mentation instructions for your computer). When working on a particular
compound you have to switch over (change directory: cd) to its directo-
ry. The compound code is not part of the file names: the file names
express the function of the files, and are identical for all compounds.
Hence the importance of using the correct directory.
Examples for PC:       CRYSIN      ATOMS       LIS1
Examples for VAX:    CRYSIN.DAT    ATOMS.DAT   LIS1.DAT


Directories and filenames for unix (aix, linex, ...) computers
 
When you start working on a new compound you must first create a
directory, probably named after your compound code CCODE, in which all
files relating to this compound are (will be) stored. When working on a
particular compound you have to switch over (change directory: cd) to
its directory. The compound code (see the implementation instructions
for unix) is part of the file names. But mind: some invisable system
files are not unique, and you may never run DIRDIF simultaneously
from(in) one directory.
Examples (CCODE=MONOS):   monos.crysin    monos.atoms    monos.lis1
 

Notes for PC users
 
The files distributed for the PC are executables, compiled by the
Salford FTN77 compiler; one of the files is: Salford DBOS/486 version
2.61 DOS extender, Serial Number 020634 Licenced for use by the Kath.
Univ Nijmegen Dir B-facult.
According to the FTN77/486 Non-Network Licence Agreement the user is
allowed to use this copy, but he shall not copy this material, or make
it available to others.
 
Hardware and software requirements for DIRDIF PC-version
Operating system:    PC-DOS or MS-DOS 3.3 or higher
Processor:     80386(SX) or 80486(SX) or Pentium.
         The use of an 80387 or 80487 co-processor (when appropriate) or
         Weitek co-processor is strongly recommended.
Memory:     at least 2 Mb internal memory
Disk space:    hard disk required, at least 4 Mb.
Video:   no special requirements, unless you want to use the plotting
         program (PLUTON: A. Spek) provided with the system. In that
         case an EGA or a VGA/SVGA monitor is required.
 

How to use PLUTON for DIRDIF results on a PC
 
At the end of a successful DIRDIF run the file CCODE.SPF is ready for
use by PLUTON. Enter at the terminal:  =====>  PLUTON CCODE
 
For a first model you may enter respectively:
labels on / stick color / plot / quit .
For a nicer plot, use: labels on / straw color / omit q / plot / quit .
Note: the file CCODE.SPF (generated by NUTS/AT2X) contains some of these
instructions at the end, which means that routinely you will get a nice
view immediately.
 
We hereby gratefully acknowledge and thank Dr. A.L. Spek from the
University of Utrecht for allowing us to use and distribute his plot
program PLUTON together with the DIRDIF program system. Normally the
program is available free of charge from the author for use within the
academic community under the condition that it is not redistributed. A
licence fee is charged to profit organizations. Therefore you are not
allowed to forward this program to others without asking explicit
permission from the author: Dr. A.L. Spek, Kristal- en Structuurchemie,
Universiteit Utrecht, Padualaan 8, 3584 CH  Utrecht, The Netherlands.
E-mail: SPEA@CHEM.RUU.NL
 
 
                                                          Contd: Page 18
------------------------------------------------------------------------
Section 7.     Acknowledgements and References
 

The following students, co-workers and colleagues have greatly
contributed to the development of DIRDIF and its sub-programs:
G. Admiraal, H.J. Behm, H.J. Bruins Slot, H.M. Doesburg, R.C.
Haltiwanger, J.H. Noordik, Th.W. Hummelink, V. Parthasarathi, P.H.J.
Prick, S.B. Sanni, G.F. Schaefer, C. Smykalla, M. Struempel, Th.E.M. 
Van den Hark, W.K.L. Van Havere.
 
The following colleagues have contributed to the implementation on
various computers:
G. Baudoux, J.P. Declercq, R. Driessens, R. Olthof-Hazekamp, A.L. Spek,
N.P.C. Walker, ...
 
For part of this research financial aid was obtaind from the Dutch
National Science Foundations FOMRE, SON and STW.
 

DIRDIF documents
 
The DIRDIF.PRIMER with a short write-up of the use of DIRDIF
The DIRDIF.HANDOUT, a two-page summary = terminal document
The DIRDIF.ORBASE-GALLERY, a visualization of the fragments available in
       the data base
The DIRDIF USER'S GUIDE is a collection of these documents and  includes 
       lecture notes with theoretical background and further information
 

Selected DIRDIF references
 
-  Program PHASEX, general procedures: Van den Hark, Th.E.M., Prick,
   P.A.J. and Beurskens, P.T. (1976) Acta Crystallogr. A32, 816.
-  Pseudo-symmetry: Prick, P.A.J., Beurskens, P.T. and Gould, R.O.
   (1983) Acta Crystallogr. A39, 570-576.
-  Statistical procedures: Beurskens, P.T., Bosman, W.P., Doesburg,
   H.M., Van den Hark, Th.E.M., Prick, P.A.J., Noordik, J.H., Beurskens,
   G., Gould, R.O. and Parthasarathi, V. (1983) Conformation in Biology,
   R. Srinivasan and R.H. Sarma, eds. (Adenine Press, New York), p. 389.
-  The DIRDIF program system, general: Beurskens, P.T. (1985)
   Crystallographic Computing, Vol. 3,  G.M. Sheldrick, C. Krueger and
   Goddard, eds. (Clarendon Press, Oxford), p. 216.
-  Program ORIENT: Beurskens, P.T., Beurskens, G., Strumpel, M. and
   Nordman, C.E. (1987)   Patterson and Pattersons, J.P. Glusker, B.K.
   Patterson, and M. Rossi, eds. Clarendon Press, Oxford), p. 356.
-  Program TRACOR: Beurskens, P.T., Gould, R.O., Bruins Slot, H.J. and
   Bosman, W.P. (1987)  Z. Kristallogr.  179, 127.
-  PHASEX phase expansion procedure: P.T.Beurskens and C.Smykalla (1991)
   Direct Methods of Solving Crystal Structures, ed.  H.Schenk,
   Plenum Press, New York and London, pp. 281.
-  Program PATTY: Beurskens, P.T., Admiraal, G., Behm, H., Beurskens,
   G., Smits, J.M.M. and Smykalla, C. (1991)   Z. f. Kristallogr.
   Suppl.4, p.99.
 
 
Reference to DIRDIF-96
----------------------

Please refer to the present program system as:
   P.T. Beurskens, G. Beurskens, W.P. Bosman, R. de Gelder,
   S. Garcia-Granda, R.O. Gould, R. Israel and J.M.M. Smits (1996).
   The DIRDIF-96 program system, Crystallography Laboratory, University
   of Nijmegen, The Netherlands.
 
========================================================================
========================================================================
===========  This is an ASCII copy of the hardcopy PRIMER  =============
========================================================================
========================================================================
