Re: [IMP-users] struggling to make structure predictions

[Ben Webb <>]

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
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle