IDEAL - INPUT FILE

IDEAL - Input file format

Data requirements:
These are designed to be simple rather than elegant. Each line is read and interpreted according to the first four characters on it. Lines relating to each set of coordinates must be given together, with the CELL line (if any) first, and the END line last. The following are the possible lines:

  1. CELL : to be followed by six numbers on the same line in free format, giving a, b, c, alpha, beta and gamma. These may be in direct or reciprocal space (A-1), with the angles either in degrees or as cosines. If no CELL is given, Angstrom-coordinates in are assumed, so if two sets are given from the same structure, the CELL line must be repeated.
  2. ATOM : to be followed by an atom name of up to four characters, and three coordinates, x, y, and z. The word ATOM is optional, but if it is omitted, the atom name must come in columns 1-4, and must, of course, not correspond to another type of card. Anything beyond the z-coordinate will be ignored.
  3. END : signals the end of a coordinate set. There must be at least two of these in any run.
  4. FINI(SH) : signals the end of the job.
  5. INVE(RT) : placed anywhere before an END-card will invert all the atoms in that set to -x,-y,-z. It may not be used in the first set.
  6. SHEL(X) : used anwhere in a run indicates that all subsequent CELL and ATOM cards will be in SHELX-format, i.e. the first number after CELL or the atom-name will be ignored. Other SHELX cards must not be present. AFIX, for example, will be treated as an atom!
  7. Lines with blanks in columns 1-4 will be ignored.

The following is a simple example file to compare two sets of atoms. Note that the order of the atoms is unimportant, only the names are compared: 

ATOM  O1  1.9046  3.4531  4.5047
ATOM  C2  1.1244  2.2765  4.2905
ATOM  O3  0.1562  2.1305  5.3469
ATOM  C4 -0.6103  3.2144  5.6631
ATOM  O4 -1.6185  3.0046  6.2954
ATOM  C5 -0.0995  4.5072  5.2557
ATOM  C6  1.2575  4.6284  4.7334
ATOM  O6  1.8640  5.6560  4.5506
END
CELL  7.544  8.576  12.014  78.01  83.36  71.41
O1   .2370   .2956   .8258
C4   .3679   .5907   .7843
O4   .4656   .6615   .7618
C5   .2929   .5148   .8982
C2   .2001   .4138   .7210
O3   .3369   .5015   .6997
C6   .2617   .3499   .9183
O6   .2582   .2612  1.0104
INVERT
END
FINISH

In this case, all eight atoms of set 1 also occur in set 2; this is not necessary; any or all sets may have extra atoms. The INVERT line will cause the enatiomorph of the atoms in set 2 to be fitted to set 1. Additional sets of coordinates may be added before the FINISH line.

Output:
For each CELL, the orthogonalisation matrix used is given. Coordinates are listed in both fractional (XF etc.) and orthogonal (XO) form. The coordinates of the initial and final fits are given relative to the first set, but with the origin at the centre of gravity. DIFF is the distance in Angstroms between the corresponding atoms in the two sets. Large values of DIFF may indicate wrongly labelled atoms or that the two structures are actually mirror images. Finally, all of the coordinates in the second or subsequent set are listed relative to the cell of the first set.