[IMP-users] Floppy bodies

[Komjati Kornel <>]

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