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
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 >
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 >
On 2/6/20 7:25 AM, Altair Hernández Chinchilla wrote: > 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
Use whatever works best for you. We generally work with hierarchies because it makes it easier to select groups of related structure particles (e.g. with IMP.atom.Selection) (and certainly PMI uses them extensively) but no need to use them for most restraints.
Ben
Hi Ben, Thanks for your answer! Kind regards, Altair
On Fri, 7 Feb 2020 at 22:48, Ben Webb ben@salilab.org wrote:
> On 2/6/20 7:25 AM, Altair Hernández Chinchilla wrote: > > 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 > > Use whatever works best for you. We generally work with hierarchies > because it makes it easier to select groups of related structure > particles (e.g. with IMP.atom.Selection) (and certainly PMI uses them > extensively) but no need to use them for most restraints. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >
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Altair Hernández Chinchilla -
Ben Webb -
Julian