Hello,
I have recently been trying to conduct flexible modeling using beads of varying size for a particular protein. I have separated the protein into 5 domains based on the PDB crystal structure, and I have already done rigid body modeling to fit the domains to an EM map we have. However, I seem to run into an issue when I try to do flexible modeling by creating bead models using the topology file. Essentially, each of the domains is coming directly from the PDB crystal structure, and I am creating beads from the residues listed there and in the FASTA file. The beads are created with a varying number of residues to reflect the size and overall flexibility of the domain. When I set up the topology file in this manner, and make sure to not invoke the rigid body or super rigid body options, I get a structure warning from IMP saying it is making the components flexible. However, I also get a warning that "No hierarchies were passed to create_flexible_beads()". I am not sure why no flexible beads are being created from the PDB/FASTA specified residues. I am using the "ToplogyReader" and the "execute_macro" functions to set up the hierarchy and the DOF for the MC simulation.
I have tried 'enable_all_movers()' to make the beads flexible, but they don't seem to exist. When I try 'dof.get_flexible_beads()' or 'dof.get_movers()', both of the lists are empty. Because the movers list is empty, I am unable to run the MC simulation macro. Could you possibly help me diagnose this problem? Is there a simple way to do the flexible bead modeling and fit it to an EM map, as I have described above? Is there some consideration I am missing in my script?
Thank you, and if you need more information on the errors or the system I am working with, I am happy to provide it.
Best,
Jacob