PRIMER file: 5-monos.txt     [ dirdif manual chapter 5 ]    15 Aug. 2008
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             Example runs on test 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

- change directory to dirdif/MONOS

- 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 some
      possibilities, in order to learn about various conventions and
      options.
- Look at the MONOS data files .
      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. 
 
Proceed to run DIRDIF with the data of test structure MONOS, solving the
structure of MONOS along six different routes, depending  on the apriory
information we assume to know:

route 1:  call program PATTY,  using DIRDIF in automatic mode   (RUN 1),
route 2:  call program PHASEX, asuming to know the S position   (RUN 2).
route 3:  call option ATMOD, then program ORIENT              (RUN 3+4).
route 4:  call program TRACOR, using one S in the origin for fun RUN 5).
route 5:  call program Orient, using three models in file ATMOD (RUN 6). 
route 6:  call program ORFLEX to create multiple models in ATMOD RUN 7).



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, 
with x=0.0 !  This site generates a mirror plane in the model.
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):
atold    atomic parameters of consecutive steps in the procedure (?)
atoms    atomic parameters of the complete structure
monos.res :  converted ATOMS file to SHELX format
ddlog    information on this run and some important data
lis1     listing file 
lis2     (ignore, use only in case of problems)
 
The information on the atold file and on the ddlog file will be extended
in following runs of DIRDIF. The files atoms, <ccode>.res, lis1 and lis2 
are overwritten in a next run. You don't have to delete any file that
has been created by this run before you run RUN 2.
 
 
RUN 2.   Route 2: option PHASEX
 
In RUN 1 the structure MONOS has been solved, but let us run some more
DIRDIF jobs in order to learn about the program.
Assume for test RUN 2 that we know the position of the sulfur atom. To
input one correct sulphur position, please, 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, crysin, fref 
 
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 re-created 
         (look at these files using your local editor):
atoms    atomic parameters of the complete structure
monos.res    converted ATOMS file to SHELX 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 ATMOD + program 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
an interactive for an interactive retrieval of the rigid fragment
from ORBASE as a set of atomic parameters (7 atoms) which is to be.
stored in file ATMOD. 
Then (RUN 4) we call an automatic run of ORIENT.
 
The following files are available for input: crysin and fref .

For RUN 3, enter at the terminal:
=====>   DIRDIF MONOS ATMOD
 
   [ at this stage, it may be convenient to open a separate WINDOW
   [ showing the file DOCS/gallery.pdf or DOCS/manual.pdf ]

In the following dialog you may also answer in lower case.
                                                         | You answer at
On the screen appears:                                   | the terminal:
                                                         |
- 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
- Schematic picture of the model. Just 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 ATMOD file with model coordinates (Cartesian) is output.
 
    =============================================================
    == Note: just in case the ORBASE file is not available, we ==
    == have supplied the ATMOD file under the name: ATMOD.BAK  ==
    == To use it, enter: copy ATMOD.bak ATMOD , and continue : ==
    =============================================================

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. 
 
The following files have been updated
           (look at these files using your local editor):
atold      atomic parameters sets of some steps in this and former runs
atmod      atomic parameters of the model in Cartesian coordinates
atoms      atomic parameters of the complete structure
monos.res  converted ATOMS file to SHELXL format
ddlog      information and data on this and preceding runs
lis1       output listing (not for printing)
lis2       (ignore, use only in case of problems)
 

Note 1: It may be possible that relative to the original input fragment
the two nitrogen atoms are placed at carbon positions, and v.v. 
This N-C interchange is the result of the ORIENT rotations of the model; 
another acceptable orientation does not have this interchange.
Note 1: The final DIRDIF result often shows an interchange of almost
equal atoms relative to the true structure. The user does the chemistry.
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[2007] RUN 5,6,7 for  Route 4,5,6 wil be described later. 

 
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