TRMX r11 r12 r13 r21 r22 r23 r31 r32 r33 t1 t2 t3
in which 'r11 r12 r13' expresses the new
a-axis in terms of the old etc.
Example:
a' =
b +
c is encoded as 0 1 1
t1 t2 t3 indicate a shift of origin after the cell transformation. The shift vector is subtracted
from the transformed coordinate data.
A TRMX (or the synonymous)
TRNS instruction may contain either 3 numbers (i.e.
translation only), 9 numbers (i.e. transformation matrix only) or 12 numbers (i.e. both
transformation and shift)
The TRMX will affect only data following it !
Symmetry operations may be protected for transformation by placing [] e.g. SPGR [C2/c].
This may be useful when the target space group is known and the transformation doesn't
seem to work otherwise (which should of course never happen ... )
The transformed data may be written out as a
.res file by clicking on the
SHELXL-res
button in the PLATON opening window (
Section 1.3.7.12) or with the keyboard instruction
CALC SHELX
2.4 - Concepts and Notions
This section details some PLATON concepts and notions needed to make use of special
program options.
2.4.1 - TRNS - The n.ijk symmetry operation on input
Atomic coordinates as found on the input file will in general be transformed as part of the
process of setting up a connected set by symmetry operations by following certain rules. In
the default automatic mode this will result in a connected set with residues properly
positioned within the unit cell range. The symmetry operation applied to the input data will
be listed under the header
move in the atomic coordinates listing and is encoded as
n.ijk.
n
stands for the number of the symmetry operation as specified on the first page of the output
listing and
ijk for the unit cell translations in the three directions relative to 555:
ijk=564
means one positive translation in the
b direction, one negative translation in the
c direction
and none in the
a direction.
The automatic mode transformation may be overruled for a given atom by preceding the
data for that particular atom with a
TRNS instruction e.g.
TRNS 3.564. This facility may be
useful to specify the part of the molecule that is to be considered as the asymmetric part of a
symmetrical molecule.
A transformation that is to be applied only to the first atom that is used as the starting point
of a new residue can be forced with a negative symmetry transformation code e.g.
TRNS
-5.354. Its position in the input stream determines the atoms to which it will apply. The
input stream may contain several
TRNS -n.ijk, each apply to the atoms that follow until
superseded by a new one. Their effect will only be on atoms that are chosen to start a new
residue. TRNS instructions can be useful to assure that water molecules are transformed to
locations where they are hydrogen bonded to the main molecule.
See also
NOMOVE (Section 2.5.1.3)
Example: shelxl.res structured input file on example.spf (with the instruction
TRNS -2.666
inserted) invoked with
platon example.spf and keyboard instructions
CALC SHELX and
END
TITL Sucrose
CELL 0.71073 10.8633 8.7050 7.7585 90.000 102.945 90.000
ZERR 1 0.0005 0.0004 0.0004 0.000 0.006 0.000
LATT -1
SYMM - X , 0.50000 + Y , - Z
SFAC C H O
UNIT 24 44 22
FVAR 1.00000
TRNS -2.666
O2 3 0.22954 0.43550 0.74766 =
11.0000 0.0277 0.0288 0.0193 -0.0013 0.0084 -0.0031
O1 3 0.17143 0.34630 0.39165 =
11.0000 0.0154 0.0131 0.0177 0.0006 0.0035 -0.0002
O3 3 0.30801 0.74770 0.70279 =
11.0000 0.0328 0.0252 0.0478 -0.0172 0.0206 -0.0099
etc ...
H611 2 0.36724 0.01189 0.11947 =
11.0000 0.0422 0.0592 0.0661 0.0164 0.0189 0.0216
HKLF 4 1 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000
will produce a new file
example.res
TITL Sucrose
CELL 0.71073 10.8633 8.7050 7.7585 90.000 102.945 90.000
ZERR 1 0.0005 0.0004 0.0004 0.000 0.006 0.000
LATT -1
SYMM - X , 0.50000 + Y , - Z
SFAC C H O
UNIT 24 44 22
FVAR 1.00000
O1 3 0.82857 1.84630 0.60835 =
11.0000 0.0154 0.0131 0.0177 -0.0006 0.0035 0.0002
O2 3 0.77046 1.93550 0.25234 =
11.0000 0.0277 0.0288 0.0193 0.0013 0.0084 0.0031
O3 3 0.69199 2.24770 0.29721 =
11.0000 0.0328 0.0252 0.0478 0.0172 0.0206 0.0099
Etc ...
H611 2 0.63276 1.51189 0.88053 =
11.0000 0.0422 0.0592 0.0661 -0.0164 0.0189 -0.0216
HKLF 4 1 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000
Where the symmetry operation
1-x, 3/2+y, 1-z was applied to
O1. All other atoms are
transformed (in this case with the same operation) to make a connected molecule.
Note:
TRNS is not a native SHELX instruction.
2.4.2 - Disorder
The program attempts to manage the problems that are encountered with several types of
disorder. Only two-fold disorder is allowed. Populations higher than 0.5 are understood as