IMP-dev September 2014

imp-dev@salilab.org

3 participants
4 discussions

rmf questions
by Yannick SPILL 19 Sep '14

19 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

2 2

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

2 4

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

2 2

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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IMP-dev September 2014