Re: [modeller_usage] Modeller Outputs TER field wrong in PDB

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

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():
https://salilab.org/modeller/9.24/manual/node181.html

	Ben Webb, Modeller Caretaker
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