mmCIF support #74
Description
from OSL:
The PDB folks are no longer releasing all proteins in PDB files. Some proteins, including those of interest to users of the PGD, are now only released in mmCIF files. To my knowledge, there are no proteins available in PDB files that are not available in mmCIF files. Therefore, the PGD should support mmCIF files instead of PDB files.
History
#1 Updated by Jack Twilley over 2 years ago
I was able to test our locally compiled DSSP binary, and the DSSP file it generated from 3CGX's mmCIF file matched that generated from 3CGX's PDB file. So that's promising.
Also, Bio.PDB was able to import multiple mmCIF files using parser.get_structure() without errors. I do not yet know if the mmCIF parser's structure differs from that of the PDB parser.
#2 Updated by Jack Twilley over 2 years ago
The Bio.PDB code that executes the DSSP binary to generate DSSP data will only process PDB, not mmCIF. I have opened an issue with the Bio.PDB folks: biopython/biopython#459 No idea how important it is to them to fix it.
#3 NOTE FROM ANDREW:
Bio.PDB is updated and now correctly deals with mmCIF files.