Approximate Molecular Symmetry Detection

Pluto recognises approximate (i.e. not necessarily crystallographic) molecular symmetry by detecting the symmetry elements existing in the molecule and then assigning a symmetry point group. The program derives a number of matrices which correspond to the symmetry operations, e.g. 2-fold rotation axis, mirror plane etc. Symmetry elements are considered as being present if sets of topologically equivalent atoms can be transformed onto their equivalent sites by the symmetry operator matrices, within practical tolerances. The default tolerances for bond lengths and angles in program are given as 0.1 Å and 5 degrees, respectively. This is an experimental feature under development.

Point Groups

Currently, the program has been designed to recognise the following point groups, this list may be extended in the future:

Operators

Molecular point group

1C(1)
2C(2), C(s), C(i)
3C(3)
4C(2v), C(2h), D(2), C(4), S(4)
5C(5)
6C(3v), C(3h), D(3), C(6), S(6)
7C(7)
8D(2h), D(2d), C(4v), C(4h), D(4), C(8), S(8)
10C(5v), C(5h), D(5), C(10), S(10)
12D(3h), D(3d), C(6v), C(6h), D(6), C(12), S(12), T
14C(7v), C(7h), D(7), C(14), S(14)
16D(4h), D(4d), C(8v), C(8h), D(8), C(16), S(16)
20D(5h), D(5d)
24D(6h), D(6d), T(h), T(d), O
28D(7h), D(7d)
32D(8h), D(8d)
48O(h)
60I
120I(h)

Typed commands

MSYM detects symmetry of molecules in the current entry, labels the molecules according to their point group and displays the symmetry elements on the molecule as planes, vectors and/or centroids, if any symmetry is detected. In the case of T, O, and I symmetries, for clarity no elements are displayed for these point groups. An molecular symmetry output file is generated. The user may either choose a file name for this output or use the default name, jobname.msy. For each entry, output includes Refcode, molecule number, molecular point group, space group, Z and Z' values and number of symmetry operations (Nmats). By default, hydrogen atoms are ignored in the symmetry detection and the number of non-hydrogen atoms is limited to 100 as the cpu time increases substantially with the number of atoms. For a molecule which belongs to an infinite point group, output will indicate as "less than 3 atoms" or "linear molecule" as appropriate.

MSYM HYDR detects symmetry of molecules in the current entry, including hydrogen atoms, although a larger tolerance is used for hydrogen atom coordinates. This is useful where the hydrogen atoms may lower the symmetry of the molecule (e.g. OH groups). A 100 atom limit applies to all atoms including hydrogens.

COMDEF AUTSYM may be used to generate a molecular symmetry output file in batch mode. After symmetry of the first molecule is detected, typing PLOT ALL, will cause Pluto to automatically run through all entries in the file and derive their symmetries. Note that the symmetry elements will not be displayed, however.

CHTL allows tolerances to be changed. This is useful for recognising molecular symmetry in a poorly-refined structure or where some atoms are distorted from the expected positions. This command only applies to the current entry (i.e. tolerances are reset on moving to another entry). Caution should be exercised, as tolerances which are too large may lead to spurious symmetry operations being found, in which case a point group cannot be derived. In some cases, it may be necessary to reduce the tolerances from their default values. In addition, because of larger errors in the derivations, sometimes the symmetry elements may not be displayed properly. This feature is under development.

TMSY detects (pseudo-)symmetry elements between chemically similar but crystallographically inequivalent molecules in a crystal structure, using the same detection algorithm as MSYM. In addition, translational symmetry elements (e.g. glide planes, screw axes) are detected.