Chem3D Users Manual - CambridgeSoft

Cartesian Coordinate Files
The Cartesian coordinate file format (Cart Coords,
Cart Coords 2) interprets text files that specify
models in terms of the X, Y, and Z coordinates of
the atoms. This file format can also interpret
fractional cell coordinates in orthogonal or nonorthogonal
coordinate systems.
Atom Types in Cartesian Coordinate
Files
Two file formats are supplied with Chem3D that
interpret Cartesian coordinate files. The difference
between the two file formats are the codes used to
convert atom type numbers in the file into atom
types used by Chem3D.
In Cartesian coordinates 1, atom types are
numbered according to the numbering used by
N.L. Allinger in MM2. These numbers are also
generally followed by the program PC Model.
In Cartesian coordinates 2, the atom type number
for all atom types is computed by multiplying the
atomic number of the element by 10 and adding the
number of valences as specified by the geometry of
the atom type. These numbers are also generally
followed by the program MacroModel.
For example, the atom type number for C Alkane (a
tetrahedral carbon atom) is 64.
To examine the atom types described by a file
format, see “Editing File Format Atom Types” on
page 241.
The Cartesian Coordinate File Format
The format for Cartesian coordinate files is as
follows:
1. The first line of data contains the number of
atoms in the model.
Optionally, you can follow the number of
atoms in the file with crystal cell parameters for
the crystal structure: a, b, c, α, β, and γ.
Following the cell parameters, you can also
include an exponent. If you include an
exponent, then all of the fractional cell
coordinates will be divided by 10 raised to the
power of the exponent.
2. The first line of a Cartesian coordinate file is
followed by one line of data for each atom in
the model. Each line describing an atom begins
with the symbol for the atom. This symbol
must correspond to a symbol in the Elements
table. The symbol can include a charge, such as
N+. The symbol is followed by the serial
number.
3. The serial number is followed by the three
coordinates of the atom. If you have specified
crystal cell parameters in the first line of the
file, then these numbers are the fractional cell
coordinates. Otherwise, the three numbers are
X, Y, and Z Cartesian coordinates.
4. Following the coordinates is the atom type
number of the atom type for this atom. This
number must correspond to the code of an
atom type record specified in the file format
atom type table. For more information, see
“Editing File Format Atom Types” on page
241.
5. Following the atom type number is the
connection table for the atom. You can specify
up to ten other atoms. The connection table
for a Cartesian coordinate file can be listed in
one of two ways: by serial number or by
position.
Connection tables by serial number use the
serial number of each atom to determine the
number that appears in the connection table of
other atoms. All serial numbers must,
therefore, be unique.
Appendices
ChemOffice 2005/Appendix File Formats • 243
File Format Examples