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 or 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 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