PRIMER 5. monos                                           file: 05-monos
[Preliminary version]           DIRDIF-2007                 28 July 2007

------------------------------------------------------------------------
PRIMER
Section 5.     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

- 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 all
      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. If you wish to have 
      a 'cold' start with MONOS: erase the DDLOG 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 prigram 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.
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).
[2007: one interchange: O <--> V ! ] 
 
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
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)
 
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
 
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, CRYSDA, BINFO 
 
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
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 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 will be.
stored in file ATMOD. 
Then (RUN 4) we call an automarit run of ORIENT.
 
The following files are available for input: CRYSIN and FREFA .

For RUN 3, enter at the terminal:
=====>   DIRDIF MONOS ATMOD
 
In the following dialog you may also answer in lower case.
                                                         | You answer at
On the screen appears:                                   | the terminal:
                                                         |
- Please give TITLE                                      | Test RUN 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
- 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.
 
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
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)
 


------------------------------------------------------------------------

[2007] RUN 5,6,7 for  Route 4,5,6 wil be described later. 

 
------------------------------------------------------------------------
