- IMP-users - salilab.org

changing the python version in IMP
by Merav Braitbard 05 Sep '19

05 Sep '19

Hi, my default version of python is 2.7, but when I tried to run imp with this version I've got an error that numpy version is old. So I tried to use python 3.7 like this: setup_environment.sh python3.7 modeling.py and I got this error: *Traceback (most recent call last): File "modeling.py", line 21, in <module> import IMP.pmi.restraints.crosslinking File "/vol/sci/bio/bio3d/meravb/Programs/imp_build_cluster/lib/IMP/__init__.py", line 11, in <module> import _IMP_kernelImportError: /vol/sci/bio/bio3d/meravb/Programs/imp_build_cluster/lib/_IMP_kernel.so: wrong ELF class: ELFCLASS64* what can I do in order to run IMP properly. Furthermore recently it takes very long time (hours) to build the IMP. Do you know why this has happened? Thanks, Merav

2 1

CrossLinkTable
by Julian 28 Aug '19

28 Aug '19

Dear IMP gurus, I'd like to get some frequency statistics for my cross-link based final model. Rather than starting from scratch, I saw tools doing more or less what I want - it seems like IMP.pmi.analysis.CrossLinkTable class methods like write_cross_link_database and get_frequency_statistics functions would be useful. A ContactMap plot would be nice but less important. To work with this class, it appears I need a single stat file, but what I have is a cluster of rmf files with a single frame each, originating from a bunch of stat files from different runs. Is there a simple way to generate a stat file from the rmfs to initialize a CrossLinkTable? Or am I going about this the wrong way? Thanks much, Julian

1 0

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

1 0

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

1 0

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

2 1

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

2 1

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

2 1

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

1 0

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/

1 0

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

2 1