Thanks a lot Julian! I'll check it out! Regards, Altair
On Thu, 6 Feb 2020 at 23:50, Julian julian.san@gmail.com wrote:
> 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 >> > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >