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