Hi Ben,

Thanks for the replay. I am newie to modeller. Do you have an example where soap_pp.Assessor class is used? (or where I can find it)

Thanks a lot for your help.

Pablo

2017-09-06 19:42 GMT+02:00 Ben Webb ben@salilab.org:

> On 8/28/17 7:46 AM, Pablo Chacon wrote: > >> I am trying to use the soap_score utility to compute the orientational >> soap protein-protein (pp) score for a set of pp decoys, but I was unable to >> find a compatible hdf5 file for pp. >> Is there any way to use the tool for pp? >> > > SOAP-PP is not orientation dependent. Its formulation is a little > different to the other SOAP potentials (it includes a pairwise term and > also an atomistic term) so I'm relatively confident that IMP's soap_score > utility won't work with it. There is support in Modeller for SOAP-PP > scoring though, and the HDF5 files for SOAP-PP are included in the Modeller > distribution. I've updated https://salilab.org/SOAP/ with this > information. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >

Hi Ben,

You are right, I only need the pairwise term and in principle the soap_score utility is exactly what I need for ranking docking solutions. My confusion was that I thought that I need to include a orientation potential file in order to get the correct soap_pp because it is an orientational dependent potential. I now realize that the default "distance" potential is already orientational.

Thanks for your help and patience,

Pablo

2017-09-07 22:08 GMT+02:00 Ben Webb ben@salilab.org:

> On 9/7/17 1:05 AM, Pablo Chacon wrote: > >> Thanks for the replay. I am newie to modeller. Do you have an example >> where soap_pp.Assessor class is used? (or where I can find it) >> > > Just to be absolutely clear here - SOAP-PP contains two scoring terms, a > SAS term that is applied to each atom, and an atomistic pairwise > statistical potential that is applied to each *pair* of atoms. IMP does > have classes to apply both terms (and the potentials themselves are also > included with IMP) but the soap_score utility only applies the pairwise > term. If you are only ranking rigid docking solutions, the atomistic term > should cancel out anyway, so it isn't needed. What do you need to do that > isn't handled already by soap_score? > > If you want to assess with both terms with Modeller, something like the > following should work (although untested): > > import modeller > import modeller.soap_pp > from modeller.scripts import complete_pdb > > env = modeller.environ() > env.libs.topology.read(file='$(LIB)/top_heav.lib') > env.libs.parameters.read(file='$(LIB)/par.lib') > > sp = modeller.soap_pp.Asssesor() > > mdl = complete_pdb(env, 'my.pdb') > atmsel = modeller.selection(mdl) > score = atmsel.assess(sp) > > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >