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 BAP54@mail.missouri.edumailto:BAP54@mail.missouri.edu
On 8/6/12 2:24 PM, Adhikari, Badri (MU-Student) wrote: > 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).
The scripts you've attached are IMP scripts. This is the Modeller mailing list. You'd probably have more luck on the IMP mailing list.
Ben Webb, Modeller Caretaker
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Adhikari, Badri (MU-Student) -
Modeller Caretaker