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
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:
Johnson City, TN