Hi IMP users,
I am currently working with no PDB structure, but with a custom artifact proteins made of concatenated beads (IMP spheres with volume). I would like to apply and integrate different type of data on it (cross linking - mass spectrometry, yeast two-hybrid, and cryoEM). I would like to ask you if should I work with hierarchies (IMP.atom.Hierarchy https://integrativemodeling.org/2.12.0/doc/ref/classIMP_1_1atom_1_1Hierarchy.htmlor IMP.core.Hierarchy) in this case, customizing my hole complex of 8 subunits with different molecules and atoms. If it is the case, how can I work on it in the way that I can parse the full molecule like: """ for molecule in root.get_children(): for atom in molecule.get_children(): do sth """ I have been trying on it, but no way to track the full hierarchy. I would appreciate some help, or just an example to how work on it. Or may be there is no sense to. For instance, the IMP.core.ConnectivityRestraint example https://integrativemodeling.org/2.12.0/doc/ref/classIMP_1_1core_1_1ConnectivityRestraint.html makes hierarchies but is not parsing the full molecule, only connecting all the beads. I would like to force it to only a pair of fragments to be connected in a certain distance. Some advice for it? Should I work on it if needing to integrate cryoEM data with IMP.pmi?
Thanks in advance!
Altair