- IMP-users - salilab.org

IMP 2.2.0 release
by Ben Webb 10 Apr '14

10 Apr '14

IMP 2.2.0 is now available. It contains a number of new features, notably support for SOAP scoring and a more reliable RMF file format. See https://github.com/salilab/imp/releases/tag/2.2.0 for the full change log. Check it out at http://integrativemodeling.org/ As always, we'll make a a 2.2.1 release in a few weeks if any significant bugs show up in 2.2.0. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

1 0

RMF error while building
by Ibai Irastorza 07 Apr '14

07 Apr '14

Hi imp users, Yesterday I had 2 running imp's in 2 computers: 2.0.1 version and the developer version downloaded from github. I deleted both (imp folder and path lines from bash) to get the 2.1.1 version because I am still using IMP.restrainer and I need rmf module to make a movie. I get this error over and over again in both computers: [ 88%] /home/bioinfo/Programs/imp/swig/IMP_rmf.impl.i:1: Error: Unable to find 'RMF.i' Running swig on restrainer Traceback (most recent call last): File "/home/bioinfo/Programs/imp-2.0.1/tools/build/make_swig_wrapper.py", line 97, in <module> main() File "/home/bioinfo/Programs/imp-2.0.1/tools/build/make_swig_wrapper.py", line 90, in main run_swig(outputdir, options) File "/home/bioinfo/Programs/imp-2.0.1/tools/build/make_swig_wrapper.py", line 47, in run_swig % (ret, " ".join(args))) OSError: subprocess failed with return code 1: swig -castmode -interface _IMP_rmf -DPySwigIterator=IMP_RMF_PySwigIterator -DSwigPyIterator=IMP_RMF_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -I../../include -I../../swig -oh wrap.h-in -o wrap.cpp-in -I/home/bioinfo/Programs/imp/include -I/usr/include /home/bioinfo/Programs/imp/swig/IMP_rmf.i make[2]: *** [src/rmf_swig/wrap.cpp] Error 1 make[1]: *** [modules/rmf/pyext/CMakeFiles/_IMP_rmf.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... Linking CXX shared library ../../../lib/libimp_domino.so Scanning dependencies of target _IMP_restrainer [ 88%] Built target imp_domino [ 89%] Building CXX object modules/restrainer/pyext/CMakeFiles/_IMP_restrainer.dir/__/__/__/src/restrainer_swig/wrap.cpp.o Linking CXX shared module ../../../lib/_IMP_restrainer.so [ 89%] Built target _IMP_restrainer ^Cmake[2]: *** [modules/core/pyext/CMakeFiles/_IMP_core.dir/__/__/__/src/core_swig/wrap.cpp.o] Interrupt make[1]: *** [modules/core/pyext/CMakeFiles/_IMP_core.dir/all] Interrupt make[2]: *** [modules/atom/pyext/CMakeFiles/_IMP_atom.dir/__/__/__/src/atom_swig/wrap.cpp.o] Interrupt make[1]: *** [modules/atom/pyext/CMakeFiles/_IMP_atom.dir/all] Interrupt I searched for the RMF.i file it is ok located in rmf/dependency/RMF/swig/RMF.i I tried with all versions (even getting the RMF_source from git to get the module), I tried to turn off the network as Jan suggested here ,I tried the developer version also, installed the doxygen 1.8.5 version also and the same error always. I don't know what I am missing because yesterday I installed the 2.1.1 and the developer version in one of the computers without problems, and today does not work. I would really appreciate your help, 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…

2 3

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…

3 3

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.

4 4

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

2 1

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

2 2

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

2 1

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 > >

2 1

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.

2 1

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

2 3