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274 discussions

IMP 2.11.1 release
by Ben Webb 18 Jul '19

18 Jul '19

IMP 2.11.1 is now available. This is a bugfix release, which fixes some issues with the build system, failures to read RMF files, and cloning of molecular hierarchies. See https://integrativemodeling.org/2.11.1/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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IMP 2.11.0 release
by Ben Webb 25 Jun '19

25 Jun '19

IMP 2.11.0 is now available. This is a bugfix and major update release. Most notably a number of new tutorials are now available covering a variety of topics from modeling complexes with IMP::pmi to writing new C++ code. The build system has also been overhauled to better support multiple versions of Python, to allow building IMP extensions modules outside of the IMP build tree, and to support using IMP as a library in other programs. See https://integrativemodeling.org/2.11.0/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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Topology colors
by Daniel Ziemianowicz 20 May '19

20 May '19

Hello, Quick question - in the topology file is "color" restricted to the names of colors as specified by Chimera? Or can we use the 6-digit hex code as well? E.g. instead of "red" use "#ff0000". I ask because of the color set in Chimera is limited to a set of specific color names, but it does allow the input of any color as specified by the hex code. Thanks, Dan

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weights testing
by Andrea Graziadei 26 Apr '19

26 Apr '19

Hello IMPers, I am continuing to working with IMP/PMI for integrative modeling of a protein complex using EM and crosslinking information. Ultimately, as in the tutorial, I have 4 sets of restraints: excluded volume, connectivity, crosslinks and gaussian. I would like to explore what weights to set. At the moment, I am doing a grid search and looking at within-simulation and between-simulation RMSD of the best models. Perhaps you can point me towards some resources or guidelines on how to optimise weights in IMP? I know this is a big topic and a big field, is there perhaps some optimisation script or some sort of wrapper you can point me towards? In general, it seems to me that in the tutorial XL, EV and connectivity restraints are left with the default weights, and the Gaussian restraint is scaled so that it has similar violation scored as the XL restraints. Is this a sort of "recommended starting point", provided I have equal confidence in XL and EM data? Additionally, I would love to implement some sort of multi-stage sampling where particles are initially fit to the EM density with low XL weights, and later refined using a higher XL weight. Is it possible to somehow pass the best energy model of one ReplicaExchange macro as the starting point of a second one? Many thanks for your input, Andrea Graziadei PostDoc, Rappsilber Group Tu Berlin

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naming subunits in IMP
by Merav Braitbard 09 Apr '19

09 Apr '19

Hi, I have a big complex and I named my chains with specific names/letters. I wrote in the topology file the chains names, but in the output the chains is alphabetical and not with the names that I want. Do you how to change it? One more question, Is there a way to save a specific frame from the rmf file as a pdb file? Thanks, Merav

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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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IMP 2.10.0 release
by Ben Webb 08 Jan '19

08 Jan '19

IMP 2.10.0 is now available. This is a bugfix and major update release. Most notably the IMP::pmi module has been overhauled; the IMP::pmi::representation::Representation class is now deprecated (and will be removed in the next release) and the IMP::pmi::topology::System class should be used instead. A legacy IMP::pmi1 module is now provided to support old published applications of IMP that use the old Representation class, but should not be used for new applications. This release also includes a number of bug fixes and performance improvements. See https://integrativemodeling.org/2.10.0/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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multifit proteomics file
by Andrea Graziadei 07 Dec '18

07 Dec '18

Hello, Apologies for the naive question, I hope this has not been asked already. I have successfully installed IMP and gone through the multifit tutorial with 3sfd. I am in the process of implementing multifit for initial fitting of our own EM density with proteomics data. However, I have a question regarding the proteomics restraint file. in the example file: |proteins| |3sfdA|1|613|nn|nn| |3sfdB|1|239|nn|nn| |3sfdC|1|138|nn|nn| |3sfdD|1|102|nn|nn| |interactions| |residue-xlink| |1|3sfdB|23|3sfdA|456|30| |1|3sfdB|241|3sfdC|112|30| |1|3sfdB|205|3sfdD|37|30| |1|3sfdB|177|3sfdD|99|30| |1|3sfdC|95|3sfdD|132|30| |1|3sfdC|9|3sfdD|37|30| |1|3sfdC|78|3sfdD|128|30| |ev-pairs| |3sfdB|3sfdA| |3sfdB|3sfdC| |3sfdC|3sfdD| It is unclear to me what each of the fields means in the "proteins" section and the meaning of the first field in the "residue-xlink" section. I assume "30" is the maximum distacnce from experimental data? What potential is used for these restraints? Many thanks in advance, Andrea

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