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273 discussions

Re: [IMP-users] Help: Troubleshooting CMake configuration errors
by Vadim Patsalo 19 Mar '13

19 Mar '13

Ben, I used the cmake command from the Wiki: https://github.com/salilab/imp/wiki/Cmake > cmake ../imp -DCMAKE_BUILD_TYPE=Debug -DIMP_DISABLED_MODULES=cgal:membrane -DIMP_PER_CPP_COMPILATION=core > CmakeSTDOUT.log 2>&1 Cmake screen output: https://gist.github.com/vadim/5c0dd1ce0d3f3c2c410c

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Help: Troubleshooting CMake configuration errors.
by Vadim Patsalo 19 Mar '13

19 Mar '13

Hello IMP community, I am following the CMake instructions here: https://github.com/salilab/imp/wiki/Cmake to compile a nightly IMP source tree. Cmake configuration fails with: "Configuring incomplete, errors occurred!" There are a number of Cmake errors in the process, and example being: > Application IMP.foxs ok > CMake Error at applications/foxs/CMakeLists.txt:48 (install): > install TARGETS given no RUNTIME DESTINATION for executable target "foxs". I am not sure which is the critical error which causes the configuration not to complete. CMakeOutput.log: https://gist.github.com/vadim/4cf6725cc29ab7953869 CMakeError.log: https://gist.github.com/vadim/2f86375106376887ab6d All the pre-requisites are installed (I believe). Using:g++ (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] --------------------------------------- Vadim Patsalo, PhD Postdoctoral Research Associate Williamson Lab, MB 20 The Scripps Research Institute La Jolla, CA 92037

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IMP FAQ
by Daniel Russel 21 Dec '12

21 Dec '12

Javi started an IMP develop FAQ in github imp wiki: <http://www.github.com/salilab/imp/wiki> You are encouraged to add questions and answers (or propose questions if you don't know the answer). As a note, one of the things that makes the github wiki quite tolerable compared to most wikis is that in addition to a nice, but fairly standard web interface, the whole wiki is a git repo. As a result, you can clone it and use any editor you want to work on the files offline and then commit and push the changes when you are done.

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svn revision number
by Benjamin SCHWARZ 05 Oct '12

05 Oct '12

In [2]: IMP.get_module_version() Out[2]: 'develop with Boost.FileSystem' I remember the good old times, when I could see the svn revision number for free. Is it hidden somewhere else nowadays ? --Ben (S.)

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Computing presence densities out of configurationSets
by Benjamin SCHWARZ 03 Oct '12

03 Oct '12

Hi list, I want to do a density based visualisation of a configurationSet, as it is described here : http://salilab.org/imp/wiki/display_ensembles Are there already any developments in IMP to do that directly, or to ease such approaches ? --Ben(S)

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Restrains beads in EM enveloppe
by Benjamin SCHWARZ 21 Sep '12

21 Sep '12

Hi list, I work on a Huge Grain Modeling approach (protein domains are represented by beads.). I need a restraint that can help me to direct and keep beads inside a given EM envelope. Do you know of any tool in the library that I can use for that ? thanks --Ben

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IMP.algebra.get_transformation_aligning_first_to_second
by unverdor＠biochem.mpg.de 30 Aug '12

30 Aug '12

Hi, we just stumbled across the same problem Ben had last year: get_transformation_aligning_first_to_second doesn't give the correct results. Can the resulting transformation be applied with get_transformed, like in the example? Or does anybody have an idea how we could get the transformation between two point sets in a different way? Thanks a lot! Carsten & Pia Date: Thu, 20 Oct 2011 10:29:14 +0200 From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> Reply-To: Help and discussion for users of IMP <imp-users(a)salilab.org> Subject: [IMP-users] does IMP.algebra.get_transformation_aligning_first_to_second minimize RMSD ? To: Help and discussion for users of IMP <imp-users(a)salilab.org> Hi list, Just confronted to something that looks like a bug, either in IMP or in my reading of the IMP manual. I'd expect the alignment of two sets of particles or vectors to minimize the RMD between the two sets, but in my case it appears the alignment produces a worse RMSD. See output underneath, and sample script attached. Considering 30 3D vectors natural rmsd between v1 and v2: 209.651290894 aligning v1 on v2... with resulting rmsd 220.458206177 running IMP version kernel SVN 10177 with Boost.FileSystem _______________________________________________ IMP-users mailing list IMP-users(a)salilab.org https://salilab.org/mailman/listinfo/imp-users

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rmf/hdf5 format
by Adhikari, Badri (MU-Student) 29 Aug '12

29 Aug '12

Hello all, While working on IMP, why do we have to use the rmf library/hdf5 file format? When do I know that I need to write my hierarchy to hdf5 file? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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pdb to restrains
by Adhikari, Badri (MU-Student) 28 Aug '12

28 Aug '12

Hello all, Can we read a pdb structure and extract restrains from the pdb? Is there a way by which we can convert pdb structures to restrain and then sample/construct structures back from just the restrains produced? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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No module named rmf
by Adhikari, Badri (MU-Student) 27 Aug '12

27 Aug '12

Following is the error I get while trying to execute the sample_0.py example. All other examples that do not use rmf module run smoothly. Everything was smooth while installing. Is there anything I missed during the installation? $../bin/python2.7 sample_0.py Traceback (most recent call last): File "sample_0.py", line 7, in <module> import IMP.rmf ImportError: No module named rmf Also that the rmf module is in the svn-trunk folder but not in the release folder. Please suggest what I should do. Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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