CCL Home Page
Up Directory CCL readme
  This directory should contain the following files:

      1) DRAWCRYS.FOR  (the main program)

      2) DRAWCRYS.EXE  (the compilled version of (1))

      3) ORFEE.INS  (the original ORFEE input instructions)

      4) CYTIDYL.ORF (ORFEE input for cytidylic acid)

      5) CYTIDYL.OUT (ORFEE output for cytidylic acid)

      6) ORFEE.FOR (original listing of ORFEE)

      The purpose here is to provide a simple method for expanding
  crystallographic information to study crystal packing.  One inputs
  the standard crystallographic coordinate information and then uses
  the program DRAWCRYS to generate a unit cell and then to add more
  unit cells onto the original unit cell.

    The output of DRAWCRYS is compatible with BABEL.  One can use
  BABEL to transform the output into a suitable format for viewing
  with a program like ALCHEMY.
    The first file contains a FORTRAN listing of the main crystal
  drawing program.  This program was compiled using MS FORTRAN 
  Powerstation on a Pentium-66 using DOS 6.2.  This compiler seems
  to use a subroutine from its own library called DOSXMSF.EXE  I've
  included this also if you want to try the DRAWCRYS.EXE without
  recompiling it yourself.  

      To use this program one needs an input file from the standard
  program ORFEE.  The input is not the same as one would use for the
  PDB files.  However one can see from a test file what the input should
  look like.  Essentially one needs the xyz coordinates of the molecule,
  the unit cell information, and the symmetry information.  The symmetry
  information reads exactly the same as the transformation in the 
  International Tables.

      One also has the option of defining the axes as the first four
  atoms (see my test file).  This is particularly useful for non-
  orthogonal axes, and allows all sorts of tricks with the program.
      ORFEE contains all sorts of useful subroutines that may be
  helpful in debugging your input.  As you can see from the test
  data I've requested bond lengths and bond angles as a check to
  see if the xyz coordinates were typed in correctly.

      I am particularly fond of option 101.  As you can see from
  the instruction this allows a search around any group of atoms.
  See the test CYTIDYL.OUT for a 4 Angstrom search of all atoms.

      To begin then:

      1) Generate an ORFEE input.  Check my trial input CYTIDYL.ORF
  to see how this is done.  I've also included the original input
  instructions for the ORFEE program.  This is called OFREE.INS.

      2) Run DRAWCRYS.  The program requests an input file.  Try
  CYTIDYL.ORF.  Then the program requests an output file.  Since
  you will probably run this through BABEL, just give it a temporary
  name like CYTIDYL.BAB.

      3) Now you must specify the transformations desired.  For
  cytidylic acid, there are 4 molecules in the unit cell.  To fill
  out the unit cell select (S) and type 02, then repeat for 03 and
      4) To generate more unit cells, just move these groups using
  option (T).  Remember the initial unit cell is 555xx.  To move
  site 01 up the  axis, select 655.  To move it down the 
  axis, select 455.  

      5) Now for some busy work.  For some graphic packages one must
  supply atom names for connectivity calculations.  Therefore one
  must have a single letter for each atom.  Sounds easy, but every
  one does this differently.  ORFEE allows 6 letters to describe each
  atom.  For a sugar hydrogen one could use HOC3'.  But someone else
  might call this C3'OH.  How can you ask the computer to tell if
  this symbol stand s for carbon, oxygen or hydrogen.  So the program
  echos the atoms name and you must type the atomic symbol.
      An obvious improvement would be to include the atomic symbol
  in the input.  

      6)  After this, the program generates an output file in BABEL
  format.  If you want to generate an ALCHEMY file with BABEL, just
  type 'babel -if cytidyl.bab -ot cytidyl.alc' at the DOS prompt.

      Suggestions/Improvements?  Let me know what doesn't work.

      Send any comments to:

                        David Close
                        Physics Dept.
                        Box 70652
                        Johnson City, TN

               e-mail   R29CLOSE@ETSU.EAST-TENN-St.EDU
               phone    423-929-5646
               FAX      423-929-6905     

Modified: Fri Mar 15 17:00:00 1996 GMT
Page accessed 8020 times since Sat Apr 17 21:34:33 1999 GMT