#4 Problems reading alt_loc entries for some mmCIF files.

[Anonymous]

I had trouble with mmLib reading alt_loc entries for mmCIF files for some PDB entries, such as 1hj9. The specific issue seems to be that the logic in L140-143 of mmLib/mmCIFBuilder.py is problematic:

if auth_count >= label_count:
self.set_atom_site_auth()
else:
self.set_atom_site_label()

Here, there are plenty of (mostly empty) 'auth' columns defined in the atom_site block of the mmCIF file, but the alt_loc for some atoms is encoded as a 'label_alt_id' field. A more robust way of figuring this out is needed, but for now, I just use the set_atom_site_label() call exclusively, though I imagine there's probably a good reason that this logic is in here in the first place.