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 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 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 > > On Jun 25, 2013, at 9:15 AM, Jan Kosinski <kosinski@embl.de > mailto: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 mailto:IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users

Yes, it does work indeed :-)

Thanks a lot!

Jan

On 06/25/2013 11:38 PM, Daniel Russel wrote: > Should be fixed in dev. > > > On Tue, Jun 25, 2013 at 10:02 AM, Jan Kosinski <kosinski@embl.de > mailto: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 mailto: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 mailto: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 >> >> On Jun 25, 2013, at 9:15 AM, Jan Kosinski <kosinski@embl.de >> mailto: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 mailto:IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org mailto:IMP-users@salilab.org >> https://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 mailto:IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users > > > > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users