J. Cheminf. 2011, 3, 33

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Crystallographic Information File (cif)

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Macromolecular Crystallographic Info (mmcif, mcif)

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Free Form Fractional format (fract)

General purpose crystallographic format

The “free-form” fractional format attempts to allow for input from a range of fractional / crystallography file formats. As such, it has only a few restrictions on input:

  • Line one of the file contains a title or comment.
  • Line two of the file contains the unit cell parameters separated by whitespace and/or commas (i.e. “a b c alpha beta gamma”).
  • Any remaining lines are parsed for atom information. Lines start with the element symbol, followed by fractional X, Y, and Z coordinates (in angstroms) separated by whitespace.

Any numeric input (i.e., unit cell parameters, XYZ coordinates) can include designations of errors, although this is currently ignored. For example:

C 1.00067(3) 2.75(2) 3.0678(12)

will be parsed as:

C 1.00067 2.75 3.0678

When used as an output format, The first line written is the title of the molecule or the filename if no title is defined. If a molecule has a defined unit cell, then the second line will be formatted as:

a b c alpha beta gamma

where a, b, c are the unit cell vector lengths, and alpha, beta, and gamma are the angles between them. These numbers are formatted as “10.5”, which means that 5 decimal places will be output for all numbers. In the case where no unit cell is defined for the molecule, the vector lengths will be defined as 1.0, and the angles to 90.0 degrees.

Remaining lines define the atoms in the file. The first column is the atomic symbol, followed by the XYZ coordinates in 10.5 format (in angstroms).

Here is an example file:

ZnO test file
3.14 3.24 5.18 90.0 90.0 120.0
O 0.66667  0.33333  0.3750
O 0.33333  0.66667  0.8750
Zn 0.66667  0.33333  0.0000
Zn 0.33333  0.66667  0.5000

Read Options

s Output single bonds only
b Disable bonding entirely