On 1/18/19 12:35 AM, dms305 wrote: > As part of my use of Modeller, I would like to access the secondary > structure information for the model. This looks to be achieved using > the SSM option to model.write_data, but this produces a file which > doesn’t contain the chain identifier.
If you're only interested in the secondary structure type, you can read this directly from the biso field - no need to use an intermediate file at all. Something like the following would work:
mdl.write_data(output='SSM') for c in mdl.chains: for r in c.residues: print(c.name, r.num, r.name, int(r.atoms[0].biso))
If you also want to look at the other columns in the SSM file, you're right - there's no chain ID output and so you'd have to use the residue index instead. I'll add chain IDs in the next Modeller release.
Ben Webb, Modeller Caretaker