Re: [modeller_usage] loop.py

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

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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