IMP-users May 2016

imp-users@salilab.org

4 participants
4 discussions

SAXS
by Georg Kempf 06 Jun '16

06 Jun '16

Hello, I am trying to combine crosslink restraints with SAXS data. I used an example script to generate a script that does the sampling with XL restraints and now I want to extend the script to test the models against the SAXS data by adding restraints e.g. radius of gyration, chi^2 value etc. I tried to use an example file but it does not really work after editing. My current problem is that I cannot load my SAXS data. I tried to use this function but it returns an error message: exp_profile = IMP.saxs.Profile.read_SAXS_file(datadirectory+'saxs.dat')) Does anyone know what's wrong here? Does anyone have other example scripts from which I can learn how to implement SAXS restraints together with XL restraints? Best, Georg

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ChimeraWriter
by Ibai Irastorza 06 Jun '16

06 Jun '16

Hello, Today I updated IMP to the last version (2.6.2) from 2.4 and I saw that IMP.display.ChimeraWriter does not exist anymore and rmf needs to be used to write the geometry to chimera format. I have been searching for examples and I think I need to use rmf_display and give "chimera" as a parameter, but I did not find any example, all the examples are with PymolWriter. Can anyone help me writing in chimera format using the rmf? And do I need to change more lines of code with this change or can I just replace "w = IMP.rmf.ChimeraWriter(storage_folder+"/"+chimera_file)" with a similar line?? thanks a lot Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…

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IMP 2.6.1/CentOS-7/Ninja (only) building issue
by Tru Huynh 25 May '16

25 May '16

Hi, I am preparing the computer lab machine for a course this summer and I am running into a strange "ninja issue". [tru@optiplex7020 ninja]$ cmake ../imp-2.6.1 -DCMAKE_BUILD_TYPE=Release -G Ninja -DIMP_MAX_CHECKS=NONE -DCMAKE_INSTALL_PREFIX=/isb2016/imp-2.6.1 -DCMAKE_INCLUDE_PATH="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include" -DCMAKE_LIBRARY_PATH="/isb2016/libTAU-1.0.1/lib;/isb2016/Python-2.7.11/lib" -DPYTHON_LIBRARY=/isb2016/Python-2.7.11/lib -DPYTHON_INCLUDE_DIR="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include/python2.7" -DLIBTAU_INCLUDE_DIR="/isb2016/libTAU-1.0.1" CMake Error: CMake was unable to find a build program corresponding to "Ninja". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool. CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_C_COMPILER_ENV_VAR CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_C_COMPILER CMake Error: Could not find cmake module file:/home/tru/ISB2016/build/ninja/CMakeFiles/2.8.11/CMakeCCompiler.cmake CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_CXX_COMPILER_ENV_VAR CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_CXX_COMPILER CMake Error: Could not find cmake module file:/home/tru/ISB2016/build/ninja/CMakeFiles/2.8.11/CMakeCXXCompiler.cmake -- Configuring incomplete, errors occurred! [tru@optiplex7020 ninja]$ type ninja ninja is /isb2016/ninja-1.7.1/ninja ninja was built from source with "./configure.py --bootstrap". I tried Ninja 1.7.1 1.6.0 and 1.5.3 without success (same error). If I run the same command without the '-G Ninja', cmake completes properly and make -j8 completes without issue. [tru@optiplex7020 fast]$ cmake ../imp-2.6.1 -DCMAKE_BUILD_TYPE=Release -DIMP_MAX_CHECKS=NONE -DCMAKE_INSTALL_PREFIX=/isb2016/imp-2.6.1 -DCMAKE_INCLUDE_PATH="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include" -DCMAKE_LIBRARY_PATH="/isb2016/libTAU-1.0.1/lib;/isb2016/Python-2.7.11/lib" -DPYTHON_LIBRARY=/isb2016/Python-2.7.11/lib -DPYTHON_INCLUDE_DIR="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include/python2.7" -DLIBTAU_INCLUDE_DIR="/isb2016/libTAU-1.0.1" -- Running check_common_problems -- Running clean_build_dir -- Running setup_cmake -- GCC version: 4.8.5 -- Enabling g++ C++11 support -- GCC version: 4.8.5 -- No conversion issue -- Doxygen is /isb2016/doxygen-1.8.6/bin/doxygen, version 1.8.6 -- Running setup_doxygen -- Python binary is /isb2016/Python-2.7.11/bin/python (version 2.7.11) -- Found PythonLibs: /isb2016/Python-2.7.11/lib (Required is exact version "2.7.11") -- Running setup -- Running setup_all -- Running making containers -- Boost version: 1.53.0 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success ... Configuring module integrative_docking ...yes -- Running setup_swig_wrappers integrative_docking -- Running IMP.integrative_docking making all header -- Running setup_swig_dependencies -- Creating thread pool with 16 threads -- Running setup_imppy -- Configuring done -- Generating done -- Build files have been written to: /home/tru/ISB2016/build/fast [tru@optiplex7020 fast]$ nice make -j8 Scanning dependencies of target IMP.kmeans-all-header Scanning dependencies of target IMP.parallel-all-header Scanning dependencies of target IMP.kernel-all-header Scanning dependencies of target IMP.test-all-header ... Best regards Tru -- Dr Tru Huynh | http://www.pasteur.fr/research/bis mailto:tru@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

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IMP 2.6.2 release
by Ben Webb 25 May '16

25 May '16

IMP 2.6.2 is now available. This corrects a few minor bugs and documentation issues in the previous release (2.6.1). In particular, we now provide packages for Ubuntu 16.04 (Xenial Xerus) and include a workaround for the buggy version of SWIG (3.0.8) included in that distribution. See https://integrativemodeling.org/2.6.2/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP-users May 2016