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 08/06/2012 07:38 PM, Adhikari, Badri (MU-Student) wrote: > 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?
I'm not sure what you're trying to do with ps=IMP.core.create_xyzr_particles(m, m.get_number_of_particles(), 1.0) since this just makes some random particles for demonstration purposes (you already have sensible atom particles in the model from the first part of the script). You probably want more MC steps too to get meaningful conformations.
> 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?
Sure, use IMP.atom.write_pdb. You already use it earlier in your script.
> 3. Is it possible to add contacts restrain (distance between atoms as a > restrain) moving forward with this approach?
Yes. Just create a restraint and add it with m.add_restraint(), same as is done for the other restraints.
Ben
participants (2)
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Adhikari, Badri (MU-Student) -
Ben Webb