February 2019 - IMP-users

IMP 2.10.1 release
by Ben Webb 26 Feb '19

26 Feb '19

IMP 2.10.1 is now available. This is a minor bugfix release. It adds support for building with OpenCV 4, and fixes some minor bugs in the create_gmm.py script and with using command line tools on systems with multiple Python installations. See https://integrativemodeling.org/2.10.1/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)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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GaussianEMRestraint of Rigid Bodies
by Lenz, Swantje 22 Feb '19

22 Feb '19

Hello, I'm trying to set up PMI GaussianEMRestraints with proteins consisting of flexible beads and rigid bodies. I followed the approach of the RNA Pol tutorial, so I used IMP.pmi.tools.get_densities and pass it on to IMP.pmi.restraints.em.GaussianEMRestraint. The GMM was created from a map via create_gmm.py?. However, it seems that only the flexible beads are being restrained and the rigid bodies are not fitted to the GMM. Any idea why this is happening? I also have a simpler test case prepared if necessary. Best, Swantje -- ________________________________ Swantje Lenz M. Sc. Biotechnology Fachgebiet Bioanalytik (TIB 4/4-3), Institut für Biotechnologie, Technische Universität Berlin Technische Universität Berlin | Gustav-Meyer-Allee 25 | Gebäude 17a | 13355 Berlin Tel +49 30 314-72906 | web: http://www.bioanalytik.tu-berlin.de/

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IMP.pmi.macros.ReplicaExchange0
by Andrea Graziadei 20 Feb '19

20 Feb '19

Hello, I am in the process of implementing some EM/crosslinking modelling using the PMI approach outlined in the tutorial for imp2.10. I have managed to get my system up and running with PMI2, but I have a couple of very basic questions in regards to the ReplicaExchange0 class in PMI and the monte carlo sampler, as I do not really understand how ReplicaExchange is implemented in PMI. Would it be possible for you to clarify how simulated annealing and monte carlo are implemented in the ReplicaExchange run in IMP, or point me towards the correct documentation? Does the macro perform a number of simulated annealing and monte carlo steps at each ReplicaExchange frame? Or does this mean that if simulated annealing is enabled, it performs simulated annealing instead of simple monte carlo? In general, what is the interplay between number_of_frames, monte_carlo_steps and simulated_annealing_minimum/maximum_temperature_nframes? At the moment, I am running a single process (so no exchange is done, I think). Additionally, I assume the weight of the restraints is constant throughout the run? Finally, I plan to implement multistate fitting. In this case, I would have one set of crosslink restraints but the system present in multiple conformations, with an EM density assigned to each state. I was wondering how XL restraints are handled in this case? Is there an OR statement applied? I hope these questions make sense, as you see I am a bit confused.. Thank you very much in advance, Andrea

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