Should be fixed in dev.
On Tue, Jun 25, 2013 at 10:02 AM, Jan Kosinski kosinski@embl.de wrote:
> Thanks! > > To answer your question about IMP version: > > I use dev versions pulled from git repo on last Friday or so. > > For imp: > $ git describe develop > 2.0.0-518-gd3125ab > > git rev-list HEAD --pretty | head > commit d3125ab77d22949e1b83b2f100d2936c7d70b088 > Author: Daniel Russel drussel@gmail.com drussel@gmail.com > Date: Thu Jun 20 17:05:56 2013 -0700 > > For RMF: > $ git rev-list HEAD --pretty | head > commit c444224ffb262a86b33edb2eaa4432971f7b0ba7 > Author: Daniel Russel drussel@gmail.com drussel@gmail.com > Date: Tue Jun 4 22:19:33 2013 -0700 > > Thanks, > Jan > > > > On 06/25/2013 06:59 PM, Daniel Russel wrote: > > BTW, I added a bug for this to the bug tracker: < > https://github.com/salilab/imp/issues/414%3E > > On Jun 25, 2013, at 9:15 AM, Jan Kosinski kosinski@embl.de wrote: > > Dear all, > > What are the methods to log the simulation frames to RMF format instead of > old Chimera style? > > I have managed to integrate RMF with IMP.restrainer but not everything > works. It seems to work with restraints like ExcludedVolume, Distance or EM > but not Y2H or PullDown - virtually all that internally are translated to > connectivity restraint make a script crashing. For example if I modify the > restrainer/nup84_complex_in_bead_representation.py to: > import IMP > import IMP.restrainer > > IMP.base.set_log_level(IMP.base.VERBOSE) > > # Create restrainer object > restrainer = IMP.restrainer.Main() > > # Add representation, restraint, optimization and display to restrainer > rep = > restrainer.add_representation(IMP.restrainer.get_example_path('input/nup84_representation.xml')) > rsr = > restrainer.add_restraint(IMP.restrainer.get_example_path('input/nup84_restraint.xml')) > > #BEGIN ADDED PART > import IMP.rmf > import RMF > > rmf= RMF.create_rmf_file('nup84_simulation.rmf') > rmf.set_description("Simulate nup84.\n") > > model = restrainer.get_model() > root_hierarchy = rep.get_root_imp_hierarchy() > > IMP.rmf.add_hierarchy(rmf, root_hierarchy) > IMP.rmf.add_restraints(rmf, model.get_restraints()) > IMP.rmf.save_frame(rmf, 0) > > os= IMP.rmf.SaveOptimizerState(rmf) > os.update_always("initial conformation") > restrainer.log = os > #END ADDED PART > > opt = > restrainer.add_optimization(IMP.restrainer.get_example_path('input/nup84_optimization.xml')) > disp = > restrainer.add_display(IMP.restrainer.get_example_path('input/nup84_display.xml'), > 'some_log_name') > > > ###=======================================================================### > # At this point all data from XML files have been placed into the model. > # Now it is possible to perform various operations on the IMP model. > > ###=======================================================================### > > # Save the initial state in Chimera format > # restrainer.log.write('initial.py') > > # Perform optimization > restrainer.optimize() > > # Save the optimized state in Chimera format > # restrainer.log.write('optimized.py') > > (note added lines and old-style Chimera stuff commented out) > > I get the following error: > Traceback (most recent call last): > File "nup84_complex_in_bead_representation.py", line 50, in <module> > IMP.rmf.save_frame(rmf, 0) > File "/home/user/software/imp_dev/lib/IMP/rmf/__init__.py", line 875, in > save_frame > return _IMP_rmf.save_frame(*args) > _IMP_base.IOException: UsageError: "Cannot write sentry value to an RMF > file." processing decorator of type Score > > WARNING No frames were saved to file "RestraintSaveLink0" even though > objects were added. > > If however I change <Y2H> node to <Distance> in input/nup84_restraint.xml > everything runs correctly and I can enjoy a working RMF file. > > Would you have any suggestions how to make RMF logging working properly? > > BTW. I am using the current dev version of IMP and RMF. > > Thank you in advance for help, > Jan > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > > > > _______________________________________________ > IMP-users mailing listIMP-users@salilab.orghttps://salilab.org/mailman/listinfo/imp-users > > > > -- > Jan Kosinski, PhD > Structural and Computational Biology Unit > European Molecular Biology Laboratory (EMBL) > Meyerhofstrasse 1 > 69117 Heidelberg > Germany > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > >