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273 discussions

Help-symmetry operation
by Joseph Eschweiler 24 May '13

24 May '13

Hello, I'm trying to implement a symmetry restraint into my python script. I would like to define a C3 symmetry between 3 of my subunits. I've looked into the TransformedDistancePairScore function and the PairsRestraint container, but I have no programming experience and am not sure how to implement these. Does anyone have a simple code for this type of restraint? Thanks, Joseph Eschweiler

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restrainer representation problem
by Ibai Irastorza 14 May '13

14 May '13

Hi IMP users, I have a fully functional script that works with IMP 1.0 libraries. When I run the same script in IMP 2.0.1 in the same computer, it throws this error: Traceback (most recent call last): File "exocyst_prt_March2013_app1.py", line 10, in <module> rep = restrainer.add_representation('input/repr_rdm_app1.xml') File "/home/ibai/imp2/lib/IMP/restrainer/__init__.py", line 464, in add_representation return _main.Main.add_representation(self, fname) File "/home/ibai/imp2/lib/IMP/restrainer/_main.py", line 17, in add_representation self.representation = XMLRepresentation(fname).run() File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 94, in run r = self._handle_node(node) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 102, in _handle_node return handler(node) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 198, in _handle_protein r = self._handle_node(child) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 102, in _handle_node return handler(node) File "/home/ibai/imp2/lib/IMP/restrainer/_xml_parser.py", line 220, in _handle_chain result = _RepChain(attrs) File "/home/ibai/imp2/lib/IMP/restrainer/_representation.py", line 204, in __init__ self.topology_file = attributes.get('topology_filename', IMP.atom.get_data_path('top_heav.lib')) File "/home/ibai/imp2/lib/IMP/atom/__init__.py", line 10284, in get_data_path return _IMP_atom.get_data_path(*args) _IMP_base.IOException: Unable to find data file top_heav.lib in [/usr/local/share/IMP]. IMP is not installed or set up correctly. And the missing data file is here: /$ sudo find -name "top_heav.lib" ./home/damien/impJune/share/imp/atom/top_heav.lib ./home/ibai/imp2/data/atom/top_heav.lib ./usr/share/imp/atom/top_heav.lib ./usr/lib/modeller9.10/modlib/top_heav.lib I don't think the code is wrong. Is the installation of imp 2.0.1 wrong? I have just installed in another laptop a fresh new IMP 2.0.1 and neither works the code. I have not read any changes about the representation module and I know the xml file is well because it works in the same computer with the IMP 1.0. Thanks in advance, ibai

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Re: [IMP-users] building error linux 64 bits
by Ben Webb 13 May '13

13 May '13

On 5/13/13 12:57 AM, Ibai Irastorza wrote: > bioinfo@bioinfo:~$ ldd Programs/Imp/lib/libimp_base.so > linux-vdso.so.1 => (0x00007fff4b1ff000) > libboost_program_options.so.1.46.1 => > /usr/lib/libboost_program_options.so.1.46.1 (0x00007f1cb65d4000) > libboost_system.so.1.46.1 => /usr/lib/libboost_system.so.1.46.1 > (0x00007f1cb63d0000) > libboost_random.so.1.53.0 => /usr/local/lib/libboost_random.so.1.53.0 > (0x00007f1cb61cc000) OK, something isn't right here. Looks like you have an incomplete copy of boost in /usr/local/lib, so it picked up boost_random from there but couldn't find boost_system, so the linker pulled in the older version in /usr/lib/. This mix of boost versions is the cause of your problem later on. You'll need to either remove the partial copy of boost 1.53 from /usr/local, or install a full copy there. 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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Re: [IMP-users] building error linux 64 bits
by Ben Webb 10 May '13

10 May '13

On 05/10/2013 12:06 AM, Ibai Irastorza wrote: > I did what you say but nothing changed. I send you the failes attached. > I don write the log in the email because of its length. Is libimp_base.so linked to libboost_filesystem? (Run 'ldd' on it.) What is Boost_FILESYSTEM_LIBRARY set to in CMakeCache.txt? Can you run 'rm lib/libimp_base.so; make VERBOSE=1 IMP.base' and show me the command it's running to build libimp_base.so? What version of IMP are you building? 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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Re: [IMP-users] building error linux 64 bits
by Ben Webb 08 May '13

08 May '13

On 05/08/2013 09:03 AM, Ibai Irastorza wrote: > it does work fine now the "cmake" line, I guess i fixed it without > noticing, but thats not the problem now, I still can't "make -j 4" In that case I suggest that in order to eliminate the "fixed it without noticing" issue, you make a fresh build directory, and run cmake && make in that directory. If it still doesn't work, send the complete output of both commands. 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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Re: [IMP-users] building error linux 64 bits
by Ben Webb 08 May '13

08 May '13

On 5/8/13 8:54 AM, Ibai Irastorza wrote: > the cmake code line fails when I try to build the "imp-2.0.0" folder > cloned from git. Fails how? 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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building error linux 64 bits
by Ibai Irastorza 08 May '13

08 May '13

Hi, I have a problem installing IMP in mu 64bits ubuntu laptop. I had no problem installing in a ubuntu 32 bits. Here are all the steps, I know some of then are redundant but wanna make sure: sudo apt-get install cmake sudo apt-get install libboost-all-dev sudo apt-get install libbz2-dev sudo apt-get install libboost-dev sudo apt-get install build-essential g++ sudo apt-get install build-essential sudo apt-get install python-dev sudo apt-get install autotools-dev sudo apt-get install swig sudo apt-get install libhdf5-serial-dev sudo apt-get install hdf5-tools sudo apt-get install zlib1g sudo apt-get install libhdf5-serial-1.8.4 sudo apt-get install libc6 git clone git://github.com/salilab/imp.git then created a folder and from there: cmake ../imp -DCMAKE_BUILD_TYPE=Release make -j 4 what am I missing?? thanks a lot! Ibai

2 1

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>.

1 0

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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