Hello all,
I am struggling to write a python program that takes protein sequence as input and produces some conformations as the output (with no any other input data).
With the help of previous replies, I tried merging the examples: “structure_from_sequence.py”, “charm_forcefield.py” and “basic_optimization.py” and wrote a script that is attached.
This script runs and produces chimera python files that I can visualize through chimera.
1. Will the script that I have prepared work as an example to produce 3D structures with just sequence as input? OR have I made any fundamental/conceptual mistakes while merging them?
2. I can produce chimera python files for each of the predicted conformations. But I want pdb files. Is it possible to do that? Are there any examples?
3. Is it possible to add contacts restrain (distance between atoms as a restrain) moving forward with this approach?
Sincerely,
Badri Adhikari
CS Graduate Student,
University of Missouri-Columbia,
Columbia, Missouri