- IMP-users - salilab.org

IMP 2.0.0 has been released
by Daniel Russel 29 Apr '13

29 Apr '13

You can download it from the website < http://www.integrativemodeling.org/download.html> or access the source from git at <https://github.com/salilab/imp.git> (use the master branch). For those of you building from source, we now use CMake to build. See < https://github.com/salilab/imp/wiki/Cmake> for more info. For the future, IMP will have releases every 6 months. In addition, we will provide patches to the latest releases as necessary to fix important bugs that are encountered. You can find some more resources in the documentation < http://www.integrativemodeling.org/2.0.0/doc/html/> and the wiki < https://github.com/salilab/imp/wiki>. If you encounter bugs or other difficulties, please open an issue on github at < https://github.com/salilab/imp/issues>, or email the imp-users list. There have been lots of improvements since 1.0. You can view the change history at <http://www.integrativemodeling.org/2.0.0/doc/html/recent.html>.

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Windows build
by Tovchigrechko, Andrey 04 Apr '13

04 Apr '13

What are your plans for supporting Windows builds? As of today, building from the head of develop branch on GitHub reveals several problems during the CMake configure phase: 1. You store symlinks in the repo. After checking out the code on Windows, they are converted to text files that contain the path of the link. There are no plans in Git to support Windows symlinks on NTFS. This also breaks Scons build. 2. Your python script that copies sources into build calls os.symlink() (easy to fix, I fixed it in my copy) 3. Somehow when CMake calls python scripts as executables, with imp_execute_process(), they do not run (nothing happens at all, no error message). The same command line works fine from Windows command window. Prepending the command with 'python' fixes it, but there is a lot of such calls in the code 4. Your various Python scripts that generate CMake files use os.path.join(), resulting in paths that mix Unix and Windows separators, such as: ${PROJECT_SOURCE_DIR}/modules\base\CMakeModules\Checkhas_auto.cmake. CMake exits with an error I also tried building on Cygwin. Compilation caused g++ segfault on latest Cygwin 1.7. Updating Cygwin to "experimental" carried the compilation further, but then it stopped with missing Python library names while linking swig generated extension. Thanks, Andrey

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Help- running IMP scripts
by Joseph Eschweiler 29 Mar '13

29 Mar '13

Hi, Our group recently had our IT staff install the nightly build IMP-SVN.v17084-el6x86_64.rpm on our linux system. The first line of our python script is simply "import IMP" and it returns ImportError: No module named IMP. The folder "IMP" is located in /usr/bin/share/IMP and contains some of the modules like "atom" but nothing simply "IMP." We've consulted with the IT staff who installed the program and he is quite confused as to what the problem is, any help would be appreciated. Thanks, Joseph Eschweiler Ruotolo Group University of Michigan

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Re: [IMP-users] Help: Troubleshooting CMake configuration errors
by Vadim Patsalo 19 Mar '13

19 Mar '13

Ben, I used the cmake command from the Wiki: https://github.com/salilab/imp/wiki/Cmake > cmake ../imp -DCMAKE_BUILD_TYPE=Debug -DIMP_DISABLED_MODULES=cgal:membrane -DIMP_PER_CPP_COMPILATION=core > CmakeSTDOUT.log 2>&1 Cmake screen output: https://gist.github.com/vadim/5c0dd1ce0d3f3c2c410c

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Help: Troubleshooting CMake configuration errors.
by Vadim Patsalo 19 Mar '13

19 Mar '13

Hello IMP community, I am following the CMake instructions here: https://github.com/salilab/imp/wiki/Cmake to compile a nightly IMP source tree. Cmake configuration fails with: "Configuring incomplete, errors occurred!" There are a number of Cmake errors in the process, and example being: > Application IMP.foxs ok > CMake Error at applications/foxs/CMakeLists.txt:48 (install): > install TARGETS given no RUNTIME DESTINATION for executable target "foxs". I am not sure which is the critical error which causes the configuration not to complete. CMakeOutput.log: https://gist.github.com/vadim/4cf6725cc29ab7953869 CMakeError.log: https://gist.github.com/vadim/2f86375106376887ab6d All the pre-requisites are installed (I believe). Using:g++ (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] --------------------------------------- Vadim Patsalo, PhD Postdoctoral Research Associate Williamson Lab, MB 20 The Scripps Research Institute La Jolla, CA 92037

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IMP FAQ
by Daniel Russel 21 Dec '12

21 Dec '12

Javi started an IMP develop FAQ in github imp wiki: <http://www.github.com/salilab/imp/wiki> You are encouraged to add questions and answers (or propose questions if you don't know the answer). As a note, one of the things that makes the github wiki quite tolerable compared to most wikis is that in addition to a nice, but fairly standard web interface, the whole wiki is a git repo. As a result, you can clone it and use any editor you want to work on the files offline and then commit and push the changes when you are done.

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svn revision number
by Benjamin SCHWARZ 05 Oct '12

05 Oct '12

In [2]: IMP.get_module_version() Out[2]: 'develop with Boost.FileSystem' I remember the good old times, when I could see the svn revision number for free. Is it hidden somewhere else nowadays ? --Ben (S.)

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Computing presence densities out of configurationSets
by Benjamin SCHWARZ 03 Oct '12

03 Oct '12

Hi list, I want to do a density based visualisation of a configurationSet, as it is described here : http://salilab.org/imp/wiki/display_ensembles Are there already any developments in IMP to do that directly, or to ease such approaches ? --Ben(S)

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Restrains beads in EM enveloppe
by Benjamin SCHWARZ 21 Sep '12

21 Sep '12

Hi list, I work on a Huge Grain Modeling approach (protein domains are represented by beads.). I need a restraint that can help me to direct and keep beads inside a given EM envelope. Do you know of any tool in the library that I can use for that ? thanks --Ben

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IMP.algebra.get_transformation_aligning_first_to_second
by unverdor＠biochem.mpg.de 30 Aug '12

30 Aug '12

Hi, we just stumbled across the same problem Ben had last year: get_transformation_aligning_first_to_second doesn't give the correct results. Can the resulting transformation be applied with get_transformed, like in the example? Or does anybody have an idea how we could get the transformation between two point sets in a different way? Thanks a lot! Carsten & Pia Date: Thu, 20 Oct 2011 10:29:14 +0200 From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Reply-To: Help and discussion for users of IMP <imp-users(a)salilab.org> Subject: [IMP-users] does IMP.algebra.get_transformation_aligning_first_to_second minimize RMSD ? To: Help and discussion for users of IMP <imp-users(a)salilab.org> Hi list, Just confronted to something that looks like a bug, either in IMP or in my reading of the IMP manual. I'd expect the alignment of two sets of particles or vectors to minimize the RMD between the two sets, but in my case it appears the alignment produces a worse RMSD. See output underneath, and sample script attached. Considering 30 3D vectors natural rmsd between v1 and v2: 209.651290894 aligning v1 on v2... with resulting rmsd 220.458206177 running IMP version kernel SVN 10177 with Boost.FileSystem _______________________________________________ IMP-users mailing list IMP-users(a)salilab.org https://salilab.org/mailman/listinfo/imp-users

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