IMP-users June 2017

imp-users@salilab.org

4 participants
2 discussions

Sigmoidal crosslinks in IMP.pmi 2.7.0
by Fergal Duffy 30 Jun '17

30 Jun '17

I am using IMP.pmi to model a protein complex using MS crosslinks. I notice that the IMP.pmi crosslinking function, IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint(), scores crosslinks basically as a linear function of crosslink distance. The crosslink length is basically irrelevant here, shorter=better. Ideally, I would like to score crosslinks as a sigmoid function, with crosslinks inside the specified 'length' dropping in score. I notice that there is a deprecated SigmoidCrossLinkMS() function in IMP, which uses an IMP.pmi.SigmoidRestraintSphere to model the crosslinks. Is there a reason this is deprecated? Should I be using it? It seems to offer functionality not available elsewhere. Regards, Fergal Fergal Duffy Postdoctoral Researcher Center for Infectious Disease Research<http://www.cidresearch.org/> 307 Westlake Ave N, Suite 500 | Seattle, WA 98109 206.256.7435 | fergal.duffy(a)cidresearch.org

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Geometrical Transformations and their effects in written files
by Kai Karius 01 Jun '17

01 Jun '17

Dear all, this is my first mail on the list, so what I am going to do is: I) try what i am trying to achieve II) what classes/methods I use Its fairly simple: I create a molecule and endow it with some structure using the provided PMI classes: s = System() st = s.create_state() m = st.create_molecule(molecule.name ,sequence=molecule.get_sequence(),chain_id=molecule.chain_id) for pdb_path,chain_id in molecule: struc = m.add_structure(pdb_path,chain_id,soft_check=True) m.add_representation(struc,resolutions=[0]) The "molecule" object is a convenience class that holds the necessary information. The other methods and objects are typical pmi elements. I create a clone, build the system and decorate the clone because I want to apply a transformation to it. I do that, afterwards i write the system to pdb: c = m.create_clone(molecule.chain_id+"_C") s.build() cx = IMP.core.XYZ(c.get_hierarchy()) IMP.core.transform(cx,g) IMP.atom.write_pdb(s.get_hierarchy(),"test_1.pdb") g rotates the clone around some axis specified elsewhere. When I look at the file I would expect two molecule in different positions, yet they sit on top of each other. What am I missing? Thanks in advance and all the best, Kai (Jans friend)

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IMP-users June 2017