IMP-users January 2016

imp-users@salilab.org

3 participants
4 discussions

how do I build working pmi rnapolii examples ?
by Isabelle Phan 25 Mar '16

25 Mar '16

Hello Ben, How do I install working examples for pmi rnapolii? I need to run the analysis on my model and could not match the IMP tutorial for rnapolii with my old code. They had diverged too much. So I installed 2.4.0 stable release. This does not seem to have working examples for rnapolii. The code only has modules/pmi/broken-examples/rnapolii I tried pulling from the development version, but that does not seem to include working examples either. Am grateful for any help, Isabelle

3 4

MP.em.EnvelopeFitRestraint class
by Karine VOLTZ 05 Feb '16

05 Feb '16

Dear IMP-users, I have a question regarding the IMP.em.EnvelopeFitRestraint class: As a simple test I just tried to evaluate this restraint with an EM density map and a set of particles corresponding to each subunits that fill the map. As coordinates for each particle, I have assigned a random vector belonging to the boundingbox of the density map. Depending on the coordinates of the particles, sometimes the restraint is correctly calculated, sometimes I get the following error message: File "/usr/local/lib/IMP-python/IMP/kernel/__init__.py", line 2183, in evaluate return _IMP_kernel.Restraint_evaluate(self, *args) _IMP_base.UsageException: Usage check failure: The point is not part of the grid Context: fit_restraint::evaluate/fit_restraint scoring::evaluate/fit_restraint scoring::do_add_score_and_derivatives/fit_restraint::add_score_and_derivatives/fit_restraint::do_add_score_and_derivatives Can somebody explain me this error? Thank you Karine

2 1

em.MapDistanceTransform class
by Karine VOLTZ 07 Jan '16

07 Jan '16

Dear IMP-users, I would like to use the em.MapDistanceTransform functionality of IMP but this class does not seem to be recognized as belonging to the em module. Can somebody give me information on the way to use this class? With my best wishes for 2016, Karine

2 1

error during installation
by ashutosh srivastava 04 Jan '16

04 Jan '16

Dear IMP users I am trying to install IMP but I keep getting following error CMake Error at modules/atom/bin/cmake_install.cmake:42 (file): file INSTALL cannot find "/home/ashutosh/softwares/imp/bin/ligand_score". Call Stack (most recent call first): modules/atom/cmake_install.cmake:45 (include) cmake_install.cmake:8645 (include) I am installing imp-2.5.0 from source to local user (I dont have root permissions). I have installed SWIG and HDF5 also locally and passed their paths as environment variables. What could be the source of this error? Kindly let me know if any other detail is required. Thank you Best Regards Ashutosh

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IMP-users January 2016