Re: [modeller_usage] Chain ID not output as part of SSM option to model.write_data

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
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