From cif to unit cell coordinates

[Heisenburger2020]

Dear Sir/Madams,

I wonder if biotitie could calculate the unit cell configuration(not bio assembly) of protein from a mmcif file with the space group, unit cell shape and asymmetry unit in mmcif file?

Best,
Jiale Zhao

[padix-key]

No, unfortunately this information is currently only obtainable from PDB files via PDBFile.get_symmetry_mates().

The reason is that it is much simpler to compute them from PDB files as the necessary transformations are already available. In CIF files these transformations need to be computed from the space group (_symmetry.space_group_name_H-M field), which is much more complex and, to be honest, I lack the experience for it.

Therefore, if you (or someone who stumbles on this issue), have more experience in the space group to transformation matrix conversion, I would appreciate a PR here.

[Heisenburger2020]

Thank you for your reply. After several days of studying, I think I have understood how to get a unit cell transformation. I will try to PR.

[padix-key]

Great! I think the aim would be to have a function get_symmetry_mates() in https://github.com/biotite-dev/biotite/blob/main/src/biotite/structure/io/pdbx/convert.py, analogous to the function in structure.io.pdb (https://www.biotite-python.org/latest/apidoc/biotite.structure.io.pdb.get_symmetry_mates.html). But for the start some private function that takes the box vectors and the space group and returns a list of rotation matrices and translation vectors would be sufficient. After that I can support you, if you like to have some guidance.