Hi Altair, We just published a paper modeling all proteasome regulatory subunits as beads. The supplement has a link to a zenodo repo with the code which might be helpful.
https://www.pnas.org/content/117/1/93.short
Julian
On Thu, Feb 6, 2020, 10:25 AM Altair Hernández Chinchilla < altairch95@gmail.com> wrote:
> 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 > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >