Menu

#4 Problems reading alt_loc entries for some mmCIF files.

open
nobody
None
5
2011-02-26
2011-02-26
Anonymous
No

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.

Discussion

Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.