  Tutorial Rigid-Body Single Crystal Refinement with FullProf
  ===========================================================

  Simple Case: Naphtalene at 5K measured on D9 (ILL)


 Step 1:  Data reduction
          ==============

          The integrated intensities corrected from Lorentz factor have been obtained from the
          diffractometer in some of the usual formats. In our case we have intensities in a file
          called napht-5k.hkl with SHELX format HKLF 4.

          Open the toolbar of FullProf and open the GUI for DataRed.
          Enter the information needed for creating a DataRed input file
            - CodeFile
            - Title
            - Cell Parameters
            - Space Group symbol
            - Wavelenght

          Use the button "Browse" for searching the file "napht-5k.hkl" that should be in the
          current directory used by the FullProf toolbar.

          Once the information is provided, save the file by clicking on the disk icon or using
          the File menu.
          For security re-open the just created file to see if everything has gone well.
          You can run the program at this point. It is a console application that runs
          from the GUI

          The program DataRed merge the reflections calculating the average of equivalent
          reflections and internal R-factors and other indicators. The output file to
          be used with FullProf has extension *.int

 Step 2:  Preparation of the relevant part of a PCR file for rigid body
          =============================================================

          If one has the geometric information concerning a particular molecule from a previous
          structural determination or from an energy minimization software one has to construct
          the piece of the PCR file containing the rigid body information.


          Mol_tpcr tool (information taken from fp2k.inf)
          =============

          Mol_tPCR is a small program to prepare Rigid body objects for FullProf
          The program, called Mol_tPCR, can be run in a console as follows:

                     d:\my_prompt> mol_tpcr  myfile

          where "myfile.cfl" is a previously existing file in wich the molecule(s) to
          be read is(are) written. The main use of this program is to prepare internal
          coordinates of a rigid group when one knows a crystal structure where this
          group is present. The internal coordinates are independent of the crystal
          structure and can be ported to a new unit cell for purposes of solving a
          new crystal structure by positioning known groups.

          An example of such a file, it can be used for testing purposes,  is given below

------------------  start File: urea.cfl -------------------------------------------
!
! Example of molecule given in a crystal
!
!
CELL     5.584001   5.584001   4.688990  90.0  90.0  90.0
!
MOLEX   8   Urea      F
!    Xc         Yc       Xc         Phi     theta    Chi     TypeAngles   TypeThermal
   0.00000  0.50000  0.32811         0.0     0.0     0.0         P          ISO
     0          0         0          0       0       0           !Refinement codes
!Atm Spe        x        y        z      N1  N2  N3    Biso      Occ
Ur1  C       0.00000  0.50000  0.32811    0   0   0   0.50000   1.00000
Ur2  O       0.00000  0.50000  0.59574    0   0   0   0.50000   1.00000
Ur3  N       0.14466  0.64466  0.17816    0   0   0   0.50000   1.00000
Ur4  N      -0.14466  0.35534  0.17816    0   0   0   0.50000   1.00000
Ur5  H       0.14261  0.64261 -0.03550    0   0   0   0.50000   1.00000
Ur6  H       0.25589  0.75589  0.28398    0   0   0   0.50000   1.00000
Ur7  H      -0.14261  0.35739 -0.03550    0   0   0   0.50000   1.00000
Ur8  H      -0.25589  0.24411  0.28398    0   0   0   0.50000   1.00000
!             x(P1)    y(P1)    z(P1)     x(P2)    y(P2)    z(P2)    x(P3)     y(P3)    z(P3)
XYZ_Frame   0.00000  0.50000  0.59574   1.00000  0.50000  0.32811   0.00000  0.50000  0.32811
!
------------------  End File: urea.mol -------------------------------------------

         The meaning of the keyword CELL and other parameters are obvious from the given names.

         The keyword MOLEX must be followed by the number of atoms in the molecule, the name
         of the molecule and the kind of coordinates provided below (F: for fractional coordinates
         with respect the the given cell, C: cartesian, Z: for Z-matrix or S: for spherical coordinates )

         The parameters Xc, Yc, Zc are the fractional coordinates of the origin of the internal
         Cartesian system with respect to the given unit cell.

         The angles Phi,Theta and Chi are Euler angles (two types, P: Phi and Theta are the polar
         spherical angles of the Z-axis of the Cartesian internal frame with respect to the
         Cartesian frame attached to the unit Cell, E: conventional Euler angles).

         The keyword "XYZ_Frame" is followed by the fractional coordinates of three points in the
         unit cell. These three points will serve to position the molecule in the crystal and to calculate
         the centre and Euler angles. The origin of the Cartesian internal system will be put in the
         third given point. The z-axis is parallel to the vector P1-P3, the x-axis lies within the plane
         (P1-P3,P2-P3), and the y-axis completes the direct frame.

         The numbers N1,N2,N3 are integers defining the connectivity of the molecule as it is conventional
         in the Z-matrix formulation. If all of them are put to zero, the program will generate automatically
         a connectivity table taking the first atom as the origin, the second along "x" and the third in
         the x-y plane. This internal Cartesian frame will be put


   Complement to the manual of FullProf concerning Rigid Bodies
   ============================================================

    - The internal coordinates of rigid body objects can now be of four
      different types:

        0: Spherical coordinates (previous versions, default)
        1: Cartesian coordinates    (KIND=1)
        2: Cylindrical coordinates  (KIND=2)
        3: Z-matrix form            (P6=4, KIND=3)

    - The angles can be given in radians (previous versions) or in degrees
    - The efficiency and convergence radius has been greatly improved
    - A small program for constructing rigid body objects adequate for
      pasting in a PCR file is now provided within the FullProf suite.
      A more sophisticated program for handling molecular objects is
      being prepared.
    - Correction of the matrix given in note of 9 October 2004. It was
      just an error on writing in the document.

     In the following example the internal coordinates of atoms of the molecular
     fragment are given in standard spherical coordinates (KIND=0) and all angles
     are given in degrees (DEG=1)

!Atom Typ       x        y        z         B      Occ       P6     THETA     PHI  Spc
!  r/xc/rho the/yc/phi phi/zc/z   X0       Y0       Z0      CHI    P16:SAT   DEG  KIND
Ur1  C       0.00000  0.50000  0.32811  0.50000  1.00000  1.00000  31.3200   42.000  0
                0.00     0.00     0.00     0.00     0.00     0.00     0.00     0.00
    0.00000    0.000    0.000  0.00000  0.50000  0.32811  -12.140    0.000     1     0
       0.00     0.00     0.00     0.00     0.00     0.00     0.00
...................
Ur3  N       0.14466  0.64466  0.17816  0.50000  1.00000                     0 0 0   0
                0.00     0.00     0.00     0.00     0.00
    1.34141  121.612   45.000
       0.00     0.00     0.00
.............................................

     In the following example the internal coordinates of atoms of the molecular
     fragment are provided in form a of a Z-matrix (P6=4, KIND=3) and all angles
     are given in degrees (DEG=1). At present the internal coordinates cannot be
     refined using the Z-matrix option. Only the orientation angles (THETA,PHI,CHI)
     and the position of the molecular origin (X0,Y0,Z0) are allowed to be refined
     when using a least-squares method.
     For using this formulation in Simulated Annealing jobs there is no restriction.

!Atom Typ       x        y        z         B      Occ       P6     THETA     PHI  Spc
!   dist   Bond-ang  Torsion-ang  X0       Y0       Z0      CHI    Connectiv DEG  KIND
Ur1  C       0.00000  0.50000  0.32811  0.50000  1.00000  4.00000  31.3200   42.000  0
                0.00     0.00     0.00     0.00     0.00     0.00     0.00     0.00
    0.00000    0.000    0.000  0.00000  0.50000  0.32811  -12.140    0.000     1     3
       0.00     0.00     0.00     0.00     0.00     0.00     0.00
Ur2  O       0.00000  0.50000  0.59574  0.50000  1.00000           1   0   0         0
                0.00     0.00     0.00     0.00     0.00
    1.25491    0.000    0.000
       0.00     0.00     0.00
Ur3  N       0.14466  0.64466  0.17816  0.50000  1.00000           1   2   0         0
                0.00     0.00     0.00     0.00     0.00
    1.34141  121.612    0.000
       0.00     0.00     0.00
Ur4  N      -0.14466  0.35534  0.17816  0.50000  1.00000           1   2   3         0
                0.00     0.00     0.00     0.00     0.00
    1.34141  121.612  180.000
       0.00     0.00     0.00
Ur5  H       0.14261  0.64261 -0.03550  0.50000  1.00000           3   1   2         0
                0.00     0.00     0.00     0.00     0.00
    1.00198  120.686  180.000
       0.00     0.00     0.00


