CrystalMaker Guide: CrystalMaker Text Files

CrystalMaker has a flexible text file format that makes it easy to create your own crystals or molecules.

Introduction to CrystalMaker Text Files

 

  You can create a text file containing crystal structure details using your favourite word processor. Alternatively, launch CrystalMaker and enter the structural details using File > New Crystal command, then save the input using File > Save As command, remembering to select the Text option.

CrystalMaker's text format (crystals) can be summarised:-

  1. Title line
  2. Unit cell parameters, a, b, c, alpha, beta, gamma
  3. Structural details, including spacegroup, range for plotting, bond specifications, etc., in any order. Each line is referred to as a "card". The type of card is indicated by a four-letter code word in UPPER CASE.
  4. "ATOM" card, followed by a listing of fractional coordinates corresponding to the asymmetric unit of a crystal. Alternatively, for a molecule or crystal fragment, the list can contain orthogonal coordinates.

(A detailed description of the control cards used is given in Appendix B of the CrystalMaker User's Guide.)

Example CrystalMaker Crystal Text Files

1. Simple Input

This file contains structural data for the mineral sphene (calcium titanite). We've requested Si-O and Ti-O bonds, with the Ca atoms left unbonded. A plot range (XYZR card) has also been entered.

TITL Sphene P2.1/a
NOTE Speer & Gibbs 1976, Am. Mineral. 61:238-247
CELL 7.069 8.722 6.566 90.0 113.860 90.0
SPGR P 21/a
BOND Si O
BOND Ti O
XYZR -0.5 1.5 -0.5 1.5 -0.5 1.5
ATOM
Ca Ca 0.2424 0.9184 0.7512
Ti Ti 0.5134 0.7542 0.2495
Si Si 0.7486 0.9330 0.7490
O O(1) 0.7499 0.8202 0.2502
O O(2) 0.9108 0.8162 0.9347
O O(3) 0.3827 0.9608 0.1459
O O(4) 0.9122 0.3165 0.4368
O O(5) 0.3813 0.4601 0.6468

2. Defining Symmetry Manually

The next example is an example of using SYMM (symmetry) cards to define the general equivalent positions, rather than specifying the conventional spacegroup symbol. Note that we have to include the lattice type, using an LATC card.

TITL Cs-Leucite @ 80 K. Tetragonal, I41/a
NOTE
Neutron powder diffraction refinement by
Palmer et al. (1997) Amer. Mineral.
CELL 13.5397 13.5397 13.7518 90.0 90.0 90.0
SYMM X, Y, Z
SYMM 1/4-Y, 1/4+X, 1/4-Z
SYMM 1/4+Y, 1/4-X, 1/4+Z
SYMM 1/2+X, Y, 1/2-Z
SYMM 3/4-Y, 1/4+X, 1/4+Z
SYMM 3/4+Y, 1/4-X, 1/4-Z
SYMM -X, 1/2-Y, Z
SYMM -X, -Y, -Z
LATC I
BOND Si O
XYZR -0.1 1.1 -0.1 1.1 -0.1 1.1
ATOM
Cs W 0.36382 0.36725 0.12017
Si T1 0.07041 0.38428 0.15683
Si T2 0.17107 0.60684 0.12687
Si T3 0.38649 0.64697 0.08203
O O1 0.13170 0.29853 0.10767
O O2 0.11643 0.49137 0.12233
O O3 0.12912 0.66251 0.22413
O O4 0.12631 0.66639 0.03492
O O5 0.28923 0.58912 0.12999
O O6 0.47933 0.61751 0.15505

Entering Molecular Data

It is also possible to use CrystalMaker's text format for molecules or crystal fragments that do not have translational symmetry. However, you must first tell CrystalMaker that your file contains molecule data by including the "MOLE" card as the first entry in the text file. You should also remember to include orthogonal coordinates for all the atoms you wish to plot.

Example CrystalMaker Molecule File

You don't have to type in every single bond: the BMAX cards included here request CrystalMaker to calculate the bonds for you. This way the computer does the hard work, not you!

MOLE CrystalMaker molecule format
TITL protonated glycine molecule
NOTE
glycine (H+)-B&S: an amino acid molecule.
!
! request a ball-and-stick model
MODL 1
!
! Bond specifications: request C-C, C-O,
! C-H, C-N, H-N and H-O bonds.
BMAX C C 0.9638
BMAX C O 0.8410
BMAX C H 0.6958
BMAX C N 0.9360
BMAX H N 0.6655
BMAX H O 0.6383
!
! Atom types listed here.
TYPE
C 0.95 0.5000 0.5000 0.5000
H 0.57 1.0000 1.0000 1.0000
N 0.95 0.0000 0.0000 1.0000
O 0.89 1.0000 0.0000 0.0000
!
! Atoms are listed using orthgonal coordinates.
ATOM
C C1 0.4737 -0.1105 -0.2455
C C11 -0.0787 0.3438 0.3863
H H1 -0.3590 -0.7214 1.1253
H H2 -1.0695 0.0747 1.1906
H H21 1.3546 0.1011 -1.0457
H H3 -1.0345 -0.5451 0.3448
H H31 -0.4404 0.8343 0.0651
H H32 0.3072 0.6438 0.8680
N N1 -0.6683 -0.2508 0.7834
O O1 0.4280 -0.8600 -0.3798
O O2 1.0059 0.4099 -0.6187

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