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274 discussions

Doxygen error with last version
by Ibai Irastorza 01 Apr '14

01 Apr '14

Hi everyone, I get this error when I run "make -j 8" both with devel version from git and with the 2.1.0 version from the web: /home/platypus/imp_dev/tools/doxygen/bin/doxygen: 1: /home/platypus/imp_dev/tools/doxygen/bin/doxygen: Syntax error: "(" unexpected make[2]: *** [doxygen/base/tags] Error 2 make[1]: *** [modules/base/CMakeFiles/IMP.base-doc.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs... I do not get that error with 2.0.1 version, but I need the RMF module to work well and I read that only works with last version... thanks a lot in advance, 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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remove DiameterRestraint
by harianto tjong 16 Mar '14

16 Mar '14

Dear IMP users or developers, I run the code example http://salilab.org/imp/2.1.1/doc/html/core_2restrain_diameter_8py-example.h… It runs smoothly. But when I add at the end of the code: m.remove_restraint(r) then it will be Segmentation fault. Anyone knows how to remove this restraint appropriately? Thank you. Best, Harianto.

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RNA / DNA in IMP?
by Barak Raveh 13 Mar '14

13 Mar '14

Anyone has experience with working with nucleic acids in IMP? Does it have any existing nucleic acids support? -- Barak

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changing the default installed /usr/share/IMP path (IMP-2.1.1-1.el5.centos.x86_64.rpm/IMP-devel-2.1.1-1.el5.centos.x86_64.rpm)
by Tru Huynh 04 Dec '13

04 Dec '13

Hello, I am trying to install the prebuilt IMP rpms for CentOS-5 x86_64 in some different place, ie /usr/ -> nfs mounted /c5/shared/imp/2.1.1-1.el5.centos.x86_64 I have rpm2cpio the contents, redefined the required PATH/PYTHONPATH but I am stuck at the /usr/shared/IMP which seems to be hardcoded in lib64/libimp_base.so file. Is there a way to override that /usr/shared/IMP path with some environment variables? or some magic IMP.base.set_data_path ? testcase: <cut imp.py> import IMP import IMP.atom import IMP.multifit m=IMP.kernel.Model() mp0 = IMP.atom.read_pdb('/Bis/home/tru/0.pdb',m) </cut> $ python imp.py Traceback (most recent call last): File "imp.py", line 5, in ? mp0 = IMP.atom.read_pdb('/Bis/home/tru/0.pdb',m) File "/c5/shared/imp/2.1.1-1.el5.centos.x86_64/lib64/python2.4/site-packages/IMP/atom/__init__.py", line 10442, in read_pdb return _IMP_atom.read_pdb(*args) _IMP_base.IOException: Unable to find data file top.lib in [/usr/share/IMP]. IMP is not installed or set up correctly. begin Model 0::do_destroy: Destroying model end Model 0::do_destroy top.lib in my setup is /c5/shared/imp/2.1.1-1.el5.centos.x86_64/share/IMP/atom/top.lib and not in /usr/share/IMP/atom/top.lib Thanks Tru -- Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/ 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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Fwd: FW: FW: Installing IMP on Ubuntu
by Nan Zhao 19 Nov '13

19 Nov '13

Finally made most modules work by installing several packages. Module CGal still could be found, after installing libcgal9. If libcgal-dev package was installed, the building can not finish with an error something like "not complete, error 2". Alan

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Re: [IMP-users] FW: Installing IMP on Ubuntu
by Nan Zhao 15 Nov '13

15 Nov '13

>Does "import IMP.multifit" work from a Python interpreter? It sounds like some of your environment variables aren't set. Did you use the setup_environment script? "import IMP.multifit" does not work. I did use setup_enviroment script. But not all modules could be found. >And they are...? Besides multifit, I also noticed that em2d, emagefit, cnmultifit, numpy, could not be found. (Many other modules and applications work well.) Alan Nan (Alan) Zhao, Ph.D. Assistant Research Professor Department of Basic Sciences College of Veterinary Medicine P.O.Box 6100 Mississippi State, MS 39762 Phone: 662-325-1208 Email: nzhao(a)cvm.msstate.edu On Fri, Nov 15, 2013 at 3:23 PM, Nan (Alan) Zhao <nzhao(a)cvm.msstate.edu>wrote: > > > -----Original Message----- > From: imp-users-bounces(a)salilab.org [mailto:imp-users-bounces@salilab.org] > On Behalf Of Ben Webb > Sent: Friday, November 15, 2013 10:14 AM > To: Help and discussion for users of IMP > Subject: Re: [IMP-users] Installing IMP on Ubuntu > > On 11/15/13 6:54 AM, Nan Zhao wrote: > > I am new to IMP and tried to install it on a Ubuntu server. It worked > > well mostly and after building, I am able to use basic applications > > and modules. However, I just noticed that not all modules are > > installed. For example, if I run multifit.py, Error shows "No module > named > multifit". > > Does "import IMP.multifit" work from a Python interpreter? It sounds like > some of your environment variables aren't set. Did you use the > setup_environment script? > > > There are more than just this one. > > And they are...? > > > /usr/local/src/imp_release/doxygen/generated/all.dox:9: warning: > > unable to resolve reference to `impcgal' for \ref command > > This is just related to the documentation - nothing to worry about. > > BEn > -- > ben(a)salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users(a)salilab.org > https://salilab.org/mailman/listinfo/imp-users > >

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Installing IMP on Ubuntu
by Nan Zhao 15 Nov '13

15 Nov '13

Hi all, I am new to IMP and tried to install it on a Ubuntu server. It worked well mostly and after building, I am able to use basic applications and modules. However, I just noticed that not all modules are installed. For example, if I run multifit.py, Error shows "No module named multifit". There are more than just this one. After building, I got some warnings as following: /usr/local/src/imp_release/doxygen/generated/all.dox:9: warning: unable to resolve reference to `impcgal' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:10: warning: unable to resolve reference to `impcnmultifit' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:16: warning: unable to resolve reference to `impem2d' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:18: warning: unable to resolve reference to `impgsl' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:25: warning: unable to resolve reference to `impmpi' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:26: warning: unable to resolve reference to `impmultifit' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:40: warning: unable to resolve reference to `impEMageFit' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:41: warning: unable to resolve reference to `impcnmultifit_tools' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:47: warning: unable to resolve reference to `impmultifit_tools' for \ref command /usr/local/src/imp_release/doxygen/generated/all.dox:50: warning: unable to resolve reference to `impsaxs_merge' for \ref command /usr/local/src/imp_release/doxygen/generated/function_example_index.md:32: warning: unable to resolve reference to `IMP::atom::Atom::get_is_setup()' for \ref command /usr/local/src/imp_release/doxygen/generated/function_example_index.md:98: warning: unable to resolve reference to `IMP::core::RigidBody::get_is_setup()' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:188: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:191: warning: unable to resolve reference to `GSL' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:192: warning: unable to resolve reference to `OpenCV' for \ref command /usr/local/src/imp_release/doxygen/generated/installation.md:193: warning: unable to resolve reference to `impmpi' for \ref command /usr/local/src/imp_release/include/IMP/algebra/vector_search.h:49: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/include/IMP/core/XYZR.h:99: warning: unable to resolve reference to `cgal' for \ref command /usr/local/src/imp_release/include/IMP/core/BoxSweepClosePairsFinder.h:22: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/include/IMP/core/CoverRefined.h:37: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp_release/include/IMP/core/RigidClosePairsFinder.h:57: warning: unable to resolve reference to `CGAL' for \ref command /usr/local/src/imp/doc/tutorial/emagefit_3sfd.dox:7: warning: unable to resolve reference to `impEMageFit' for \ref command /usr/local/src/imp/doc/tutorial/multifit_3sfd.dox:7: warning: unable to resolve reference to `impmultifit_tools' for \ref command /usr/local/src/imp/doc/tutorial/cnmultifit_groel.dox:7: warning: unable to resolve reference to `impcnmultifit_tools' for \ref command Does any one know what the problem could be? Thanks. BTW, I just built it at a local directory but did not install it. I change environment variables whenever I use it.

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How to represent a protein-protein interaction network in IMP
by Hongzhu Cui 01 Nov '13

01 Nov '13

Hi, all, Recently, I have a project with IMP. Basically, we need to represent a protein-protein interaction network in IMP, and then we add some restraints to see how we could optimize this network. But I stuck on this problem, and I did not find any similar example in the Manual documentation. Thanks & Regards, Hongzhu

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IMP 2.1 release
by Daniel Russel 24 Oct '13

24 Oct '13

IMP 2.1 has been released. You can either get the source from the master branch (https://github.com/salilab/imp/tree/master) or binary installers from the downloads tab (http://integrativemodeling.org/download.html). See the release notes (https://github.com/salilab/imp/releases/tag/2.1.0) for a list of changes.

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Installing IMP on Ubuntu 12.04
by Steven Howell 10 Sep '13

10 Sep '13

Greetings IMP users, I am failing to successfully setup IMP 2.0.1 on my Ubuntu 12.04 system. Following the directions in the IMP documentation, I installed the mandatory packages - cmake - libboost-all-dev - libhdf5-serial-1.8.4 - swig as well as the optional packages - gsl-bin - ann-tools - libcgal8 - google-perftools When I run, 'cmake ../imp -DCMAKE_BUILD_TYPE=Release', I get the fatal error: -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS) CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE): Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS) I attempted installing different libhdf5 versions, lam, openmpi, and mpich, but received the same error for each. Additionally, all of optional packages I installed fail to be detected. Initially gsl and cgal are both detected but then upon configuration they are no longer found. ... -- Different data/build_info/sorted_modules +cgal +gsl ... -- Configuring module cgal ... CGAL not found Different data/build_info/sorted_modules -cgal ... -- Configuring module gsl ... GSL not found Different data/build_info/sorted_modules -gsl ... Is this a problem with a different native installation path for programs in Ubuntu vs Fedora/RedHad? What is the best work around to overcome these errors? Thank you for any help. Steven Howell Ph.D. Candidate Department of Physics The George Washington University Corcoran 203, 725 21st St, NW Washington, DC 20052 Lab: 202.994.3414

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