PRIMER file: 6-final.txt    [ dirdif manual chapters 6-8 ]  15 Aug. 2008

       Dirdif manual chapter 6=Problems, 7=Notes, 8=References           
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Chapter 6.     How to interpret the results,
               trouble shooting, how to restart

In case of problems: email to PTBeurskens [AT] hetnet.nl

Too slow?
---------

Some options may take a long time to get to the final structure:
- many heavy atoms with comparable interatomic distances may result in
  up to 50 atoms-sets which all may have to be expanded to completeness,
- or a small molecular fragment which may fit in different orientations
  and at different positions in the unit cell may lead to many trial
  structures, and many of them have to be expanded to completeness;
- and the same is true if you subject many different molecular fragments
  the the vector search procedure.
In those cases the time consuming factor is in the recycling procedure.
Have patience: at the end the best solution so far will be recycled and
delivers the final structue.
 
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 NORECY). 
The final <ccode>.res file 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. As a 
      consequence, many orientations are acceptable, and for each orie-
      entation many position may be accepted by TRACOR, which all have 
      to be analized! Try to find  a bigger fragment with more charac-
      teristic 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.)

[2008: at present LIS1 and LIS2 give too much ... to be shortened ! ]  
[2008: ignore other files such as LIS3, LIS4, LIS5, ATPAT, ATTEM,...]
    

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 !).
 

[ 2008: 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;
the new version is more reliable indeed, but we would like to do better.
We hope to have an inproved procedure in the near future. ]   



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Chapter 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. 
 

 
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: all file names are in lower case, although written in this            manual in capitals! The file names express the function of the
        files, and are identical for all compounds.
        Hence the importance of using the correct directory.
Example for PC and unix:   
        the file with name 'crysin' is written here as CRYSIN
Example for VAX: the file 'CRYSIN.DAT' is witten here as CRYSIN .

 
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) has prepared a WINDOWS version.


[ 2008: 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 ??? ] 
 


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Chapter 8.
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                 Acknowledgements and References


 
The following PhD-students (a), co-workers (b) and special guests (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.
 

 
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-2008
 
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-2008 , Crystallography Laboratory, 
   Radboud University Nijmegen, The Netherlands.
 

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End of PRIMER files             DIRDIF-2008                 15 Aug. 2008
                                      
                            
For theoretical backgroud,  see MANUAL.pdf   ( stored in dirdif / DOCS )
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