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,


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()

sp = modeller.soap_pp.Asssesor()

mdl = complete_pdb(env, 'my.pdb')
atmsel = modeller.selection(mdl)
score = atmsel.assess(sp)

ben@salilab.org                      https://salilab.org/~ben/
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