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:
- 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.
- 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.
- END : signals the end of a coordinate set. There must be at
least two of these in any run.
- FINI(SH) : signals the end of the job.
- 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.
- 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!
- 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.