CrystalMaker Guide: MacMolecule 1.x Data Files

A text format used by MacMolecule version 1.x.

MacMolecule is a program designed for creating 3-d-images of molecules. Program versions up to and including 1.7 were freeware, and their file format is supported by CrystalMaker (more recent versions of MacMolecule are no longer freeware, and their more complex file format is not supported by CrystalMaker).

A sample MacMolecule 1.x file, for the molecule glycine is given below:-


C; glycine H+
2
;model
BS
C = 1.5, 0.6 (.5,.5,.5)
O = 1.4, 0.58 (1.,0.,0.)
N = 1.5, 0.6 (0.,0.,1.)
H = 0.90, 0.36 (1.0, 1.0, 1.0)
C1 : -3.49503 1.79605 2.15052
C11 : -4.56421 0.74904 1.99995
H1 : -6.12061 1.89748 2.79283
H2 : -6.34809 0.23019 2.87950
H21 : -1.79454 2.28689 1.44555
H3 : -5.30122 0.99524 3.90571
H31 : -4.14040 -0.23229 2.19028
H32 : -4.95760 0.75616 0.99245
N1 : -5.64483 0.98849 2.95291
O1 : -3.56196 2.69996 2.94043
O2 : -2.50337 1.59972 1.31374
;BONDS
C1, C11
C1, O1
C1, O2
C11, H31
C11, H32
C11, N1
H1, N1
H2, N1
H21, O2
H3, N1
·· glycine
·· The amino acid glycine is the smallest of the 20 common amino acids found in proteins. The color scheme used to designate atoms is as follows: gray = carbon, blue = nitrogen, red = oxygen, white = hydrogen.

CrystalMaker imports all the data, including atom colours, radii, bonding, and any notes (these are the lines prefixed by pairs of bullets). Lines beginning with a semicolon ";" are comments.

The file's structure can be divided into three parts:-

  1. header information listing atom types, their space-filling radii, ball-and-stick radii, and colours (the red, green, blue colour fractions).
  2. Listing of all atoms in the molecule. For each atom a "site code" comprises the one-character atom type and a number. This is followed by the orthogonal coordinates.
  3. Listing of all bonds

You may save a Crystal as a "molecule" in MacMolecule format, using the Export Molecule command from the File menu. A text file is generated, which can be read directly by the MacMolecule program. Note that because MacMolecule represents atom types by single letters, the total number of atom types is limited to 26.

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