November 2013 - IMP-users

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