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.
On 9/24/20 7:35 AM, Jeff Reneker via modeller_usage wrote: > 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:
The other thing you need to change is the range of residues to refine. It is rather unlikely that your structure has a loop at exactly the same numbered residues as the example.
> KeyError: 'No such residue: 19:'
So in your structure you don't have a residue numbered 19 in a chain with no ID. You'll need to fill in the actual residue range, for example '1:A' for the residue numbered 1 in the chain labeled A.
Ben Webb, Modeller Caretaker
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