October 2011 - IMP-users

IMP cannot find Modeller 9.10 script - Regular Expression problem?
by João Rodrigues 23 Oct '11

23 Oct '11

Dear all, I tried to install IMP today in our cluster and I ran into a small problem with MODELLER. IMP could not find MODELLER, despite the directory and all the paths being perfectly fine. I double checked the modeller_test.py in scons_test/ and I found that the regular expression looking for mod9v10 instead of mod9.10. After changing the expression all went well. Maybe this changed with the last version of MODELLER. Just letting you know for future reference! An additional question, should I use the version 1.0 or the SVN? Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao

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does IMP.algebra.get_transformation_aligning_first_to_second minimize RMSD ?
by Benjamin SCHWARZ 20 Oct '11

20 Oct '11

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

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IMP-1.0-Stable Installation Ubuntu 10.04 Help
by Martin Turk 11 Oct '11

11 Oct '11

Dear imp users and developers, I need some help with compiling the source code on Ubuntu 10.04 I tried compiling imp with: >scons prefix=/installation/folder build=debug install and the only imp binaries being generated are foxs and protein_ligand_score. the only error I get is: """ sh: Syntax error: Bad fd number """ and the graphviz, gslcblas and modeller dependencies are missing otherwise the installation finishes without errors. Since Ubuntu has system libraries in a different place than Fedora I tried compiling imp by specifying libpath and linking it to python. What is odd is that graphviz and gslcblas are not found when I specify libpath /usr/lib/graphviz/ /usr/lib/libgslcblas.so.0 >scons -j 16 libpath=/usr/lib:/usr/lib64 path=/usr/bin pythonpath=/usr/lib64/python2.6 prefix=/home/turk/imp build=debug install again I assume the installation directory is missing some content ../bin: protein_ligand_score foxs ../lib64/python2.6/site-packages: IMP _IMP_algebra.so _IMP_atom.so _IMP_benchmark.so _IMP_container.so _IMP_core.so _IMP_display.so _IMP_domino.so _IMP_em.so _IMP_example.so _IMP_gsl.so _IMP_helper.so _IMP_misc.so _IMP_restrainer.so _IMP_saxs.so _IMP.so _IMP_statistics.so after adding site-packages to the $PYTHONPATH python import imp gives me: i>>> import IMP Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/turk/imp/lib64/python2.6/site-packages/IMP/__init__.py", line 25, in <module> _IMP = swig_import_helper() File "/home/turk/imp/lib64/python2.6/site-packages/IMP/__init__.py", line 17, in swig_import_helper import _IMP ImportError: libimp.so: cannot open shared object file: No such file or directory Now I don't know what to try next and if playing with swig will bring me any further -> the email :-) All suggestions are welcome :) Martin

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