November 2019 - IMP-users

Maximum distance restraint between spheres
by Altair Hernández Chinchilla 04 Dec '19

04 Dec '19

Hi IMP users, I want to create pairwise distance restraints between IMP particles (spheres XYZR of a given radius) with a maximum distance condition.So I want a given sphere to be in a range between 0 and max distance of 17 Aº. How can I do it in IMP? Given a set of sphere pairs, and a distance between them, how can I apply a IMP function to force a maximum distance restraint in a similar way then a Harmonic function? f = IMP.core.Harmonic(float(tag_list[1]), float(tag_list[2])) s = IMP.core.DistancePairScore(f) r = IMP.core.PairRestraint(model, s, (bait_p, tag_p)) How can I substiute the IMP.core.Harmonic with a maximum distance function? Thanks in advance! Altair

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Ambiguous restraints
by Francesco RAIMONDI 05 Nov '19

05 Nov '19

Dear all, I have a set of MS/XL restraints which I'd like to use to predict the structure of a putative homodimeric protein. Some of the XL are expected to happen within the same chain, others between the two distinct chains of the homodimer. The way I tackled the ambiguity issue so far is to explicitly generate all the possible XL/chain combinations and use this expanded list as an input for an adapted version of the human complement modeling script ( https://salilab.org/Complement) using IMP v2.9. Is there a better way to deal with ambiguity in IMP? I also found the AmbiguousCompositeRestraint <https://integrativemodeling.org/2.6.1/doc/ref/classIMP_1_1pmi_1_1restraints…> class, but didn't yet manage to find an example script using it. I'd be grateful for any suggestions you could provide me in this respect. Thanks so much and all the best, Francesco

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Compiling a module out of tree
by Patrick Goetz 04 Nov '19

04 Nov '19

I'm trying to incorporate an out of tree IMP module called bayesianem. What I thought should be possible is to install the IMP Ubuntu 18.04 binary package, build bayesianem from source, and add it, but am running in to some problems. According to the IMP documentation (https://integrativemodeling.org/2.11.1/doc/manual/uselibrary.html) "When IMP is built or installed, it creates a CMake file called IMPConfig.cmake which contains information about how IMP was configured and where all the parts of IMP can be found." Unfortunately I could not find such a file anywhere on the system, but the bayesianem cmake script is clearly looking for it. Excerpted from bayesianem's source dir CMakeLists.txt: find_package(IMP REQUIRED) include(${IMP_USE_FILE}) and if I try and do the build I get: -------------------------------- By not providing "FindIMP.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "IMP", but CMake did not find one. Could not find a package configuration file provided by "IMP" with any of the following names: IMPConfig.cmake imp-config.cmake -------------------------------- I also cloned the IMP git repo, but couldn't find anything there, either. The "Building modules out of tree" page (https://integrativemodeling.org/2.11.1/doc/manual/outoftree.html) talks about a FindIMP.cmake file, but I couldn't find this anywhere either. Presumably I am doing something wrong. Can someone give me some pointers? The bayesianem git repo (https://gitlab.pasteur.fr/rpellari/bayesianem) is pretty sparse on documentation. Thanks.

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