This command assesses the quality of the selected atoms in the model using the provided assessor object. Typically this is used for SOAP scoring, with assessor being soap_loop.Scorer() or soap_protein_od.Scorer().
Assessment uses the standard MODELLER energy function, so any of the arguments accepted by Selection.energy() can also be used here. See Selection.assess_dope() for more details on this and schedule_scale.
Any of the assessor objects accepted by this function can also be used for automatic assessment of each AutoModel or LoopModel model; see Section 2.2.3 or Section 2.3.3 for examples.
# Example for: Selection.assess(), soap_protein_od.Scorer() from modeller import * from modeller.scripts import complete_pdb from modeller import soap_protein_od env = Environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Set up SOAP-Protein-OD scoring (note: if assessing multiple models, it is # best to create 'sp' just once and keep it around, since reading in the # potential from disk can take a long time). sp = soap_protein_od.Scorer() # Read a model previously generated by Modeller's AutoModel class mdl = complete_pdb(env, '../atom_files/1fdx.B99990001.pdb') # Select all atoms in the first chain atmsel = Selection(mdl.chains) # Assess with the above Scorer try: score = atmsel.assess(sp) except ModellerError: print("The SOAP-Protein-OD library file is not included with MODELLER.") print("Please get it from https://salilab.org/SOAP/.")