December 2010 - IMP-users

add_partial_profiles
by Robert Fenwick 21 Jan '11

21 Jan '11

Hi, I am having a bit of a tough time with writing a script and wondered if someone could help. I have installed the latest nightly builds and am trying to write the following: I wish to loop over n structures, calculate the summed partial saxs profile. I hope to achieve this using the attached code and example structures. I think that I should use the add_partial_profiles function, however I can not get it to work the way that I would like. Is there a way to access the values in the predicted saxs profiles using the python interface? Here is my current code, but it does not work as I would expect. Bryn R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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single_prot_fft_fit
by Benjamin SCHWARZ 14 Dec '10

14 Dec '10

Hi list, I am trying to run the single_prot_fft_fit software for some times now with no success. I looked into the code but could not find a quick fix. I would greatly appreciate if somebody could help me get the program running. The soft was built out of IMP svn 7513, and my command line is : /usr/local/IMPsvn/imp-latest/modules/multifit/bin/single_prot_fft_fit subCplx-18A.mrc 2 18 0.25 /home/schwarz/TFdata/struct-C-term.pdb 300 --n-hits 10 --output Cter--solutions.txt --sol taf6-Cter--fitted-solution- --cc-map Cter--fit-CC-map.map --local I have tried to run this soft on three machines : * Linux 2.6.32-21-generic #32-Ubuntu SMP Fri Apr 16 08:09:38 UTC 2010 x86_64 GNU/Linux The process simply stops after a few iteration, having received a SiGKILL signal according to gdb. * Linux 2.6.24-23-server #1 SMP Thu Nov 27 18:45:02 UTC 2008 x86_64 GNU/Linux Computation seems ok for 300 rotations, but when launched in more real conditions (12000 rotations), the machine becomes unstable apparently because the process asks more and more memory (43Gb at the time we had to restart the machine) * Linux hpc-n48 2.6.18-164.6.1.el5.centos.plus #1 SMP Wed Nov 4 09:31:39 EST 2009 x86_64 x86_64 x86_64 GNU/Linux The program stops on a Segmentation fault (core dumped) with the lowest bt level being : #0 0x00002aee817bfe3f in IMP::multifit::FFTFitting::get_correlation_hit_map() const () from /home/lbm/schwarz/BenInstalls/Installs/imp-latest/lib64/libimp_multifit.so --Ben

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import fails
by Robert Brynmor Fenwick 13 Dec '10

13 Dec '10

Hi, I have managed to build the python interface with swig, but fail to import IMP from python. I am rather sure that I have installed the modules, however I am unsure where I have to point my PYTHONPATH to pick them up. The other problem might be that I don't know which version of python the modules have been installed. How can I work out which version and the location of the python executable for which the modules were build? Many thanks, Bryn

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Re: [IMP-users] numerical bug
by Robert Brynmor Fenwick 13 Dec '10

13 Dec '10

Hi, I think that I have found a small numerical bug. I can not work out how to debug this as my knowledge of c++ is not what is needs to be. I encounter the error using the python interface with the latest nightly build. To reproduce the error you can play with the two files and code attached. The file that works with the code is 433.pdb. The file that fails is 434.pdb. The traceback appears as: Traceback (most recent call last): File "bug_case.py", line 30, in <module> surface_area = s.get_solvent_accessibility(IMP.core.XYZRs(particles)) File "/opt/imp/lib/python2.5/site-packages/IMP/saxs/__init__.py", line 428, in get_solvent_accessibility def get_solvent_accessibility(self, *args): return _IMP_saxs.SolventAccessibleSurface_get_solvent_accessibility(self, *args) _IMP.UsageException: Passed index not in grid (17, 2, 3) I suspect it is a numerical instability somewhere as I have a test case that fails where I can modify the file in two ways to create a file that works. A) I generate a sorter fail (434.cut) case by: tail -228 434.pdb > 434.cut B) This calculation will proceed if I generate a slightly shorter file (i.e. remove the first ten lines). This case is generated by: tail -218 434.pdb > 434.cut C) The strange part is the calculation will also proceed if the only the first 100 lines are used (i.e. keeping the part that I removed in B ) This case is generated by: tail -228 434.pdb | head -100 > 434.cut Any suggestions would be greatly appreciated. Bryn -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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