PRIMER  6, 7, 8. Problems, notes, references              file: 06-final
[Preliminary version]                                       28 July 2007
                            DIRDIF-2007
------------------------------------------------------------------------
PRIMER
Section 6.     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 in LIS1 will be of help. lf necessary, restart
DIRDIF to find some more atoms ( use: DIRDIF CCODE FOUR NORECY). The 
final XYZN file, renamed to INS, is ready for use by the program SHELXL.
 
Trouble shooting
----------------
 
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 structures.
 
1.    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.
 
2.    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 should
      not cause problems at the next run! 
 
3.    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, probably we can learn from it.
 
4.    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.
 
5.    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. And we wish to improve the message.
      -  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 symbol-consistency decreases to below 0.50
      -  .... the number of participating reflections is 'normal' ...
      -  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.)

[2007: at present LIS1 and LIS2 give too much ... to be shortened ! ]  
 

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 (ORIENT), or with mofified CRYSIN data .
 
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/SHIFT.
 
Note: it is easy to solve a space group uncertainty by restarting DIRDIF
using different space groups   
(just modify the space group in the CRYSIN file !).
 

[ 2007: the distinction between atoms with almost the same scattering
power (C <-> N,  N <-> O, S <-> P, ...) is reduced in the new DIRDIF
version: our former procedures too often led to erroneous results;
we hope to have an inproved procedure in some months time. ]   




========================================================================

PRIMER  7, 8. Notes, references                           file: 06-final
[Preliminary version]                                       28 July 2007
                            DIRDIF-2007
------------------------------------------------------------------------
PRIMER
Section 7.           Notes for various computers


 
Some technical details are given in the various readme-, contents-, IMPLEM- and EXEC- files, when relevant for the implementation of the distributed DIRDIF 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. When working on a particular compound you have to switch over (change directory: cd) to its directory. 

Filenames for PC and VAX computers:
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

Filenames for unix (aix, linex, ...) computers:
The compound code 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
 
 
Hardware and software requirements for DIRDIF PC-version [ 2007: ??]
Operating system: we have been working with Windows-2000 and WINDOWS-XP,
    using the MSDOS prompt ( Windows > instruction processor ).
    Dr Louis Ferrugia (Glasgow) will soon care for a WINDOWS version.
Video:   no special requirements.



[ 2007: exit ?] How to use PLUTON (A. Spek) 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
[ end of PLUTON ---> the input to PLATON will be investigated ??? ] 
 


========================================================================

PRIMER  8. References          DIRDIF-2007                file: 06-final
[Preliminary version]                                       28 July 2007
                            
------------------------------------------------------------------------
PRIMER
Section 8.             Acknowledgements and References


 
The following PhD-students (a), co-workers (b) and guests/colleagues (c) have greatly contributed to the development of DIRDIF and its programs:

a. H.J. Bruins Slot, H.M. Doesburg, Th.W. Hummelink, O.R. Israel,
   E.J.W. Lam, P.H.J.Prick, Th.E.M. Van den Hark,   
b. G. Admiraal, H.J. Behm, W.P. Bosman, J.H. Noordik, C. Smykalla,
c. R.C.Haltiwanger, V. Parthasarathi, S.B. Sani, G.F. Schaefer,
   M. Strumpel,  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, ...

Special thanks for technical advice and for peparing the WINDOWS version of DIRDIF are due to 

   L.J. Farrugia .

For part of this research financial aid was obtaind from the Dutch
National Science Foundations FOMRE, SON and STW.
 

DIRDIF documents (n = 1,2,3,..., * = intro, options, ..., PATTY, ....)
 
The PRIMER with a short write-up of the use of DIRDIF (files -n-*)
The MANUAL with theoretical backgtround (files dirdif/DOCS/n-*)
The ORBASE-GALLERY, a visualization of the fragments available in
       the data base.
 
 
Selected DIRDIF references    [ 2007 ... to be updated ] 
 
-  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.
-  Program BIJVOET 
 
Reference to DIRDIF-99
 
Please refer to the present program system as:

   P.T. Beurskens, G. Beurskens, R. de Gelder, J.M.M. Smits, 
   S. Garcia-Granda & R.O. Gould ,
   DIRDIF-2007 , Crystallography Laboratory, 
   Radboud University Nijmegen, The Netherlands.
 

========================================================================

End of PRIMER files             DIRDIF-2007 
[Preliminary version]                                       28 July 2007
                            
For theoretical backgroud, see MANUAL files  ( stored in dirdif / DOCS )
------------------------------------------------------------------------
========================================================================