- IMP-dev - salilab.org

Python 3 support
by Ben Webb 12 Dec '14

12 Dec '14

Just FYI, latest IMP in git should now configure and build successfully if your 'python' binary is actually Python 3 (as with any nonstandard Python, you may need to set the cmake PYTHON_INCLUDE_DIR and PYTHON_LIBRARY variables to tell it where the associated headers and library are). Note that IMP itself doesn't fully work yet (there are still some issues with string typemaps, most likely because in Python 3 all strings are Unicode). The plan is to have our Python code run both in Python 2 and Python 3 (as opposed to maintaining a Python 2 version and a Python 3 version). This isn't too onerous since we don't support ancient versions of Python (older than 2.6) any more anyway. If you have Python code in IMP, I've modified it to work with both Python 2 and 3. You'll notice the major change is that "print" is no longer a statement in Python 3 (it's a function). So you have to say print("foo") rather than print "foo". I added "from __future__ import print_function" in IMP Python modules that use print so this will behave identically in Python 2 and 3. Other differences are fairly minor (e.g. 'xrange' is no more - use 'range' instead; some functions return iterators rather than lists in Python 3 so you have to wrap them with list() if you explicitly want the Python 2 behavior). Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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IMP 2.3.1 release
by Ben Webb 01 Dec '14

01 Dec '14

IMP 2.3.1 is now available. This is a bug fix and minor update release. Most notably two complete modeling examples that use the IMP::pmi module are now fully functional: modeling of the Nup84 subcomplex of the nuclear pore complex and of RNA Polymerase II. See https://github.com/salilab/imp/releases/tag/2.3.1 for the full change log. Check it out at http://integrativemodeling.org/ Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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has anyone tried compiling IMP on OS X 10.10 (Yosemite)?
by Charles Greenberg 24 Oct '14

24 Oct '14

Just curious if anyone's had an issue... Charles Greenberg Graduate student in biophysics @ UCSF Laboratory of Andrej Sali Cell: 561-531-9411

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IMP 2.3.0 release
by Ben Webb 24 Oct '14

24 Oct '14

IMP 2.3.0 is now available, containing bug fixes and updates. Most notably the experimental IMP::pmi module is now available. This provides a variety of high-level Python classes to simplify the construction of a modeling protocol in IMP. One recent use of PMI is the modeling of the Nup84 subcomplex of the nuclear pore complex. We also now provide binary packages for Ubuntu LTS and 64-bit Windows. See https://github.com/salilab/imp/releases/tag/2.3.0 for the full change log. Check it out at http://integrativemodeling.org/ Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Preparation for 2.3 release
by Ben Webb 02 Oct '14

02 Oct '14

So, it's about time for the next IMP release. Unless there are good reasons not to, I'll go ahead and do that in a week or two. If you made any big changes since the 2.2 release, please make sure there's a description of what you changed in the changelog: http://integrativemodeling.org/nightly/doc/html/changelog.html PMI people: there are still a bunch of broken tests and examples in PMI. It would be great if at least some of those could get fixed before the release. ;) Not a blocker for release though, as I think PMI would still be considered "experimental" at this point. If you need time for any cleanups or bigger changes, please let me know ASAP. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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rmf questions
by Yannick SPILL 18 Sep '14

18 Sep '14

Hi I have two questions regarding RMF files 1) What happens if a program that carries an open rmf3 file handle gets killed? Is the rmf file likely to be corrupted? or is this only going to affect the last frame? 2) I use the following code to reprocess trajectories, reading an old rmf file and writing a new one. write_traj is called each time a new frame is to be written in the RMF file. Frames are written sequentially, so I guess the set_current_frame(frameid) is kind of superfluous. def _write_traj_rmf(self, infile, instep, outfile): import RMF #make sure infile is open if infile not in self.traj_handles_in: src = RMF.open_rmf_file_read_only(infile) self.traj_handles_in[infile] = src src = self.traj_handles_in[infile] #make sure outfile is open if outfile not in self.traj_handles_out: dest = RMF.create_rmf_file(outfile) self.traj_handles_out[outfile] = dest RMF.clone_file_info(src, dest) RMF.clone_hierarchy(src, dest) RMF.clone_static_frame(src, dest) dest = self.traj_handles_out[outfile] #clone frame frameid = src.get_frames()[instep-1] src.set_current_frame(frameid) dest.add_frame(src.get_name(frameid), src.get_type(frameid)) RMF.clone_loaded_frame(src, dest) Does that sound ok to you? The reason I'm asking, is I get a problem with the written coordinates. They seem to be wrapped when they are too big, e.g. like in a periodic box. Any clues appreciated. Yannick

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slow molecule building
by Yannick SPILL 18 Sep '14

18 Sep '14

Hi there #read in protein model = IMP. Model() mhd = IMP.atom.read_pdb(pdb_name, model, IMP.atom.NonWaterNonHydrogenPDBSelector()) ff = IMP.atom.get_heavy_atom_CHARMM_parameters() top = ff.create_topology(mhd) top.add_atom_types(mhd) bonds = top.add_bonds(mhd) angles = ff.create_angles(bonds) dihedrals = ff.create_dihedrals(bonds) Why is this last line so much slower than the others? It's sad, because it takes up most of the time in the construction of a protein hierarchy. thanks! Yannick

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status of Rosetta integration from IMP
by Barak Raveh 11 Sep '14

11 Sep '14

Hi all, I recall Javi worked some on integration of Rosetta from within IMP, anyone knows what's the status of it? (= is it functional, tested?) -- Barak

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standard force fields in IMP eg CHARMM
by Barak Raveh 10 Sep '14

10 Sep '14

IMP supports CHARMM right? Is it any specific standard CHARMM or other force field? Does it include an implicit water model, accounting for solvation effects? Thanks! Barak

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hybrid monte carlo
by Yannick Spill 24 Aug '14

24 Aug '14

Hi there does anyone use isd::HybridMonteCarlo ? Yannick

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