May 2013 - IMP-users - salilab.org

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

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