June 2016 - IMP-users

save values of RestraintsScoringFunction to RMF
by Jan Kosinski 24 Jun '16

24 Jun '16

Hi, Is it possible to save the total score to the RMF file with IMP.rmf.SaveOptimizerState? Basically, I am saving a Monte Carlo trajectory with restraints like this: rmf = RMF.create_rmf_file('out.rmf') IMP.rmf.add_hierarchy(rmf, hierarchy) IMP.rmf.add_restraints(rmf, restraints) opt_state = IMP.rmf.SaveOptimizerState(model, rmf) opt_state.update_always("initial conformation") opt_state.set_period(10) my_score_function = IMP.core.RestraintsScoringFunction(restraints, "scoring function") o = IMP.core.MonteCarlo(model) o.add_optimizer_state(opt_state) o.set_scoring_function(my_score_function) Then I can nicely see the changes in the values of individual restraints using Chimera RMF viewer. But, I would like to see also how the my_score_function value changed over the optimization. Is it possible with IMP.rmf.SaveOptimizerState? Thanks in advance, Jan

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SAXS
by Georg Kempf 06 Jun '16

06 Jun '16

Hello, I am trying to combine crosslink restraints with SAXS data. I used an example script to generate a script that does the sampling with XL restraints and now I want to extend the script to test the models against the SAXS data by adding restraints e.g. radius of gyration, chi^2 value etc. I tried to use an example file but it does not really work after editing. My current problem is that I cannot load my SAXS data. I tried to use this function but it returns an error message: exp_profile = IMP.saxs.Profile.read_SAXS_file(datadirectory+'saxs.dat')) Does anyone know what's wrong here? Does anyone have other example scripts from which I can learn how to implement SAXS restraints together with XL restraints? Best, Georg

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ChimeraWriter
by Ibai Irastorza 06 Jun '16

06 Jun '16

Hello, Today I updated IMP to the last version (2.6.2) from 2.4 and I saw that IMP.display.ChimeraWriter does not exist anymore and rmf needs to be used to write the geometry to chimera format. I have been searching for examples and I think I need to use rmf_display and give "chimera" as a parameter, but I did not find any example, all the examples are with PymolWriter. Can anyone help me writing in chimera format using the rmf? And do I need to change more lines of code with this change or can I just replace "w = IMP.rmf.ChimeraWriter(storage_folder+"/"+chimera_file)" with a similar line?? thanks a lot Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…

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