Re: [modeller_usage] Modeller Outputs TER field wrong in PDB
To: Pedro Guillem <>
Subject: Re: [modeller_usage] Modeller Outputs TER field wrong in PDB
From: Modeller Caretaker <>
Date: Thu, 18 Jun 2020 10:03:57 -0700
Cc:
On 6/18/20 5:06 AM, Pedro Guillem wrote:
The weird part is that in my original PDB, the TER lines (6 in total)
are not followed by anything. They just read TER.
After performing mutations with modeller and saving the file, the output
of the 6 TER lines has additional columns.
Is there a particular reason for modeller to be doing this? (I can
provide the input file and output files)
I don't see how that's weird. You gave Modeller an invalid PDB file and
it made a best effort to read it anyway. It output a valid PDB. If for
some reason your pipeline needs invalid PDB files, mangle them with a
Perl or Python script to remove the extra fields from the TER records.
Alternatively, if you don't need the TER records at all, you can set
no_ter=True when you call model.write():