- IMP-users - salilab.org

Regarding IMP run
by subhomoi borkotoky 26 Apr '12

26 Apr '12

Dear all, I have the IMP to my Ubuntu 11.10 system. But I don't know how to use it even though I looked into IMP<http://salilab.org/imp/nightly/doc/html/namespaceIMP.html>Documentation . Please let me know how can I run the example scripts. what command should I write in terminal. Please help me. -- Thanks and Regards, -------------------------- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry

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protein structure from amino acid sequences with IMP
by Adhikari, Badri (MU-Student) 13 Apr '12

13 Apr '12

Hello all, I am configuring IMP as non-root user in 3 of our redhat servers. My goal, for now, is to generate extended chain structures from amino acid sequences. I am able to run the following test examples that come with the IMP installation (credit goes to Ben and Daniel): i) test_charmm_atom.py ii) test_charmm_parameters.py iii) test_charmm_topology.py However, I am unable to run the examples in http://salilab.org/imp/nightly/doc/html/atom_examples.html#charmm_forcefield The most useful example for me would be structure-from-sequence. I get the following errors: $ python /rose/space1/imp/examples/structure-from-sequence.py Traceback (most recent call last): File "/rose/space1/imp/examples/structure-from-sequence.py", line 4, in <module> topology = IMP.atom.CHARMMTopology(IMP.atom.get_all_atom_CHARMM_parameters()) AttributeError: 'module' object has no attribute 'get_all_atom_CHARMM_parameters' $ python /rose/space1/imp/examples/charm-forcefield.py Traceback (most recent call last): File "/rose/space1/imp/examples/charm-forcefield-atom.py", line 10, in <module> ff = IMP.atom.get_heavy_atom_CHARMM_parameters() AttributeError: 'module' object has no attribute 'get_heavy_atom_CHARMM_parameters' $ python /rose/space1/imp/examples/molecular-hierarchy.py residue #16 of name "LYS"Added particle for 0...1 It looks like we need to supply the charm forcefield related files as well. I am wondering on the following questions as google does not seem to be helpful. (1) What file/files and parameter file/files do we need to run these examples? (2) Where do we place the files? (3) How to generate those files for the sequences that I have? 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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protein structure generation from sequences with IMP
by Adhikari, Badri (MU-Student) 10 Apr '12

10 Apr '12

Hello all, We are working on a project in which we need to generate protein models from the amino acid sequences, using IMP. After reading on the IMP website, I can see that this tool primarily deals with different data sources. But, still I believe that this tool could be useful for us as we might need to add more information later. Have you ever tried generating models (like pdb files) with just amino acid sequences using IMP? If you have anything that could be helpful to me please help. Warm Regards, 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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Python wrapper error after IMP installation
by Adhikari, Badri (MU-Student) 10 Apr '12

10 Apr '12

Hello all, We installed IMP in one of our servers by building the source code files. I do not have root access on the servers. It looks like I need to use the atom module and so after installation, I tested the installation with the files in the test directory inside the atom module's directory. I can run the files like test_bd.py and test_charmm_atom.py run smooth, but files like test_charmm_parameters.py throw the following error. RuntimeError: Unknown error caught by Python wrapper Details of the error message is attached. Please help! Warm Regards, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri Cell: 573 639 2847 BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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ImportError: No module named IMP
by Adhikari, Badri (MU-Student) 28 Mar '12

28 Mar '12

Hello everyone, I installed IMP and tried to execute a sample python script sample.py using the command: python sample.py I keep getting ImportError that looks like in the image below. [Description: cid:image001.png@01CD0D1B.B639C5D0] I do not have root access in the server and I have installed all other prerequisites (swig, boost and scons). I downloaded IMP at http://salilab.org/imp/get.php?pkg=1.0/download/imp-1.0.tar.gz Has anyone faced this error before. Please help! ---------------------------------------- Warm Regards, 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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IMP Survey Reminder
by Charles Greenberg 12 Mar '12

12 Mar '12

Hi all, If you haven't had a chance yet, please fill out the IMP survey (link below). We will be discussing the survey results at our upcoming lab retreat, and we'd like to have as many opinions as possible. The results will help us decide future directions for IMP and improve its usability. https://docs.google.com/spreadsheet/viewform?formkey=dFZaOGlEa2hYUmE5d1N3SU… Thanks again! --Charles

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IMP Survey 2012
by Charles Greenberg 08 Mar '12

08 Mar '12

Hello IMP users, We've put together a little survey about IMP: its features, usability, documentation, etc. If you could take the time to fill it out, we'd love to get your opinions on how we can improve IMP. The survey is anonymous of course. Here is the link: https://docs.google.com/spreadsheet/viewform?formkey=dFZaOGlEa2hYUmE5d1N3SU… Thanks! Charles Greenberg Sali Lab, UCSF

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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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