Following the example in “Refining an existing PDB file” I want to “refine a region of an existing PDB file without comparative modeling.” The first thing I want to do is to get the loop.py script in the examples to work for any other structure. The only change I made is in this block of code from loop.py where I substitute 6aa0 for 1fdx as follows:

m = MyLoop(env,

           inimodel='1fdx.B99990001.pdb',   # initial model of the target

           sequence='1fdx',                 # code of the target

           loop_assess_methods=assess.DOPE) # assess loops with DOPE

#          loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop

m = MyLoop(env,

           inimodel=‘6aa0.pdb',             # initial model of the target

           sequence=‘6aa0',                 # code of the target

           loop_assess_methods=assess.DOPE) # assess loops with DOPE

#          loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop

Then, I copy the 6aa0.pdb file to the appropriate directory. This is the error message at the tail end of the output:

Traceback (most recent call last):

  File "loop.py", line 35, in <module>

    m.make()

  File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 37, in make

    self.build_seq(self.inimodel, 1)

  File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 169, in build_seq

    atmsel = self._check_select_loop_atoms()

  File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 398, in _check_select_loop_atoms

    atmsel = self.select_loop_atoms()

  File "loop.py", line 18, in select_loop_atoms

    return selection(self.residue_range('19:', '28:'))

  File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 329, in residue_range

    start = self.residues[start]._num

  File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 259, in __getitem__

    (self.offset, self.length, self.suffix))

  File "/usr/lib/python3.6/dist-packages/modeller/util/modutil.py", line 23, in handle_seq_indx

    int_indx = lookup_func(*args)

  File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 323, in _indxres

    raise KeyError("No such residue: %s" % indx)

KeyError: 'No such residue: 19:'

So, I’m not sure what the deal is because that’s how new I am to Modeller. Thanks, JR.