Systematically translate _symmetry.space_group_name_H-M to set of coordinate transforms

Question

[khouli]

Given an mmcif file, how can I systematically convert any _symmetry.space_group_name_H-M value into a set of coordinate transformations on the fractional coordinates of a structure?

At the moment I'm not even sure where I can find a definitive listing of all values that could be used in _symmetry.space_group_name_H-M. Obviously the values are limited by the possible symmetry groups but my problem is that I'm not sure where to find a comprehensive list of the text values that might be used for _symmetry.space_group_name_H-M. This seems like something that's hiding in an IUPAC table somewhere but I don't know where.

Answer 1

[wojdyr]

The most official list of space group names is probably in the International Tables for Crystallography. But you may find some special things in the PDB that are not in the tables. The latest PDBx/mmCIF dictionary (v5 RC) enumerates all allowed values. That should be all that you can find in PDB:

http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_symmetry.space_group_name_H-M.html

"A 1" "A 1 2 1" "A 2" "B 1 1 2" "B 2" "B 2 21 2" "C 1 2 1" "C 1 21 1" "C 2" "C 2 2 2" "C 2 2 21" "C 2(A 112)" "C 21" "C 4 21 2" "F 2 2 2" "F 2 3" "F 4 2 2" "F 4 3 2" "F 41 3 2" "H 3" "H 3 2" "I -4 c 2" "I 1 2 1" "I 1 21 1" "I 2" "I 2 2 2" "I 2 3" "I 21" "I 21 21 21" "I 21 3" "I 4" "I 4 2 2" "I 4 3 2" "I 41" "I 41 2 2" "I 41 3 2" "I 41/a" "P -1" "P 1" "P 1 1 2" "P 1 1 21" "P 1 2 1" "P 1 21 1" "P 1 21/c 1" "P 1 21/n 1" "P 2" "P 2 2 2" "P 2 2 21" "P 2 21 2" "P 2 21 21" "P 2 3" "P 21" "P 21 2 2" "P 21 2 21" "P 21 21 2" "P 21 21 2 A" "P 21 21 21" "P 21 3" "P 21(C)" "P 3" "P 3 1 2" "P 3 2 1" "P 31" "P 31 1 2" "P 31 2 1" "P 32" "P 32 1 2" "P 32 2 1" "P 4" "P 4 2 2" "P 4 21 2" "P 4 3 2" "P 41" "P 41 2 2" "P 41 21 2" "P 41 3 2" "P 42" "P 42 2 2" "P 42 21 2" "P 42 3 2" "P 43" "P 43 2 2" "P 43 21 2" "P 43 3 2" "P 6" "P 6 2 2" "P 61" "P 61 2 2" "P 62" "P 62 2 2" "P 63" "P 63 2 2" "P 64" "P 64 2 2" "P 65" "P 65 2 2" "R 3" "R 3 2"

To get the list of operations you may:

• use a library (cctbx or sglite or another one),
• or use a table (many macromolecular crystallography programs, in particular the ones from CCP4, use a file named symop.lib for it),
• or just use _pdbx_struct_oper_list from your mmCIF file.

Edit: the enumeration vanished from the PDBx/mmCIF v5 dictionary