Hi all,
My name is Kornel and I am trying to define a protein as a chain of rigid and floppy bodies. With the help of the online manual I worked out how to define rigid bodies, but for floppy bodies I have not found a solution.
My sample topology looks like this: |component_name|domain_name|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian| |CHAIN_A| RIGID_1 |fasta.txt| ID:A |protein.pdb |A| 121,150| 0| 30|0| |CHAIN_A| FLOPPY_1 |fasta.txt| ID:A |protein.pdb |A| 151,180| 0| 5|0| |CHAIN_A| RIGID_2 |fasta.txt| ID:A |protein.pdb |A| 181,220| 0| 30|0| |CHAIN_A| FLOPPY_2 |fasta.txt| ID:A |protein.pdb |A| 221,280| 0| 5|0|
And the modeling.py looks like this: m = IMP.Model() topology = IMP.pmi.topology.TopologyReader(topology_file) domains = topology.get_components()
rigid_bodies = [["RIGID_1"],["RIGID_2"]]
bm = IMP.pmi.macros.BuildModel(m, component_topologies=domains, list_of_rigid_bodies=rigid_bodies)
So my question is: what is the correct way to define domains as floppy bodies?
Thanks, Kornel