Re: [modeller_usage] Chain ID not output as part of SSM option to model.write_data
To: dms305 <>, "" <>
Subject: Re: [modeller_usage] Chain ID not output as part of SSM option to model.write_data
From: Modeller Caretaker <>
Date: Fri, 18 Jan 2019 10:23:41 -0800
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.