October 2015 - IMP-users

how do I build working pmi rnapolii examples ?
by Isabelle Phan 25 Mar '16

25 Mar '16

Hello Ben, How do I install working examples for pmi rnapolii? I need to run the analysis on my model and could not match the IMP tutorial for rnapolii with my old code. They had diverged too much. So I installed 2.4.0 stable release. This does not seem to have working examples for rnapolii. The code only has modules/pmi/broken-examples/rnapolii I tried pulling from the development version, but that does not seem to include working examples either. Am grateful for any help, Isabelle

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restraint based on pre-calculated scores
by Jan Kosinski 28 Oct '15

28 Oct '15

Hi, I have a custom MonteCarlo mover that randomly samples positions of a rigid body from predefined list of transformations. Each transformation corresponds to some position, and for each position I have precalculated a score. Now I would like to have a restraint that scores the positions generated by the mover according to these precalculated scores. The restraint would have to find out which transformation was used for the move, get the index of the transformation in the list and then get the score. Would you have a suggestion how to implement this? I can store the current index in the mover object but then I don't know how to access the movers from the restraint object. Thanks in advance, Jan

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question about running PMI
by Jason Schmidberger 27 Oct '15

27 Oct '15

Hello, I am new to the imp-users mailing list. I am having trouble running PMI. I am following the online RNA Polymerase example (http://integrativemodeling.org/2.5.0/doc/manual/rnapolii_stalk.html) and adapting it to suit my own protein complex. When I run the modeling.py script, I seem to get as far as defining my x-links, then the program optimizes floppy bodies, lists all my proteins, then crashes. The crash takes place with the following error; (after x-linking information) Generating a NEW crosslink restraint with an uniqueID 45 -------------- ISDCrossLinkMS: generating cross-link restraint between ISDCrossLinkMS: residue 89 of chain mol1d and residue 559 of chain mol2c ISDCrossLinkMS: with sigma1 1.000000 sigma2 1.000000 psi 0.05 ISDCrossLinkMS: between particles mol1d_89_pdb and mol2c_536-585_bead_floppy_body_rigid_body_member ========================================== optimize_floppy_bodies: optimizing 49 floppy bodies mol2a_1 mol2a_2 mol2a_3 mol2a_4 mol1b_1 mol2c_1 mol2c_2 mol2c_3 mol2c_4 mol1d_1 mol3_1 mol3_2 mol4f mol4g mol4h mol4i mol4j mol4k mol4l mol4m will scale target mass by 454684.664 mass_scale=target_mass_scale) File "/usr/local/lib/IMP-python/IMP/isd/gmm_tools.py", line 29, in decorate_gmm_from_text weight=float(fields[2]) IndexError: list index out of range WARNING Object "linker_restraints" was never used. See the IMP::Object documentation for an explanation. Can anyone advise me what the issue here is? Does it relate to my target GMM file? I am at a loss. Yours, Jason

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