Dear Ben, very simple question . I have used DOPE assessment, but in which file can I find the assessment results for the models? It's not in resulted PDB, there is only objective function.Where can I find those DOPE and GA341 values?

I have used the next Python script for the assessment: # Loop refinement of an existing model from modeller import * from modeller.automodel import *

log.verbose() env = environ()

# directories for input atom files env.io.atom_files_directory = ['.'] # Read in HETATM records from template PDBs env.io.hetatm = True

# Create a new class based on 'dopehr_loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(dopehr_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # One loop from residue 19 to 28 inclusive return selection(self.residue_range('92:', '111:'))

m = MyLoop(env, inimodel='3mhj.pdb', # initial model of the target sequence='3mhj' # code of the target ) assess_methods=(assess.DOPE, assess.GA341) # assess each loop with DOPE

m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 20 # index of the last loop model m.loop.md_level = refine.slow_large # loop refinement method

m.make()

Should those scores be available as molpdf values in .log file?

Best regards, Andrew

01.11.2011, 22:55, "Modeller Caretaker" modeller-care@salilab.org:

>  On 11/01/2011 10:28 AM, Andrew Voronkov wrote: >>   how on your opinion modeller objective function correlates with >>   quality of the models. For example I have objective function value >>   1730 for one modelk and -750 which as I understand reflects free >>   energy. Does it mean that  I shouldn t consider the first one at >>   all? >  The Modeller objective function is simply a measure of how many >  restraints were violated in building your model. While the score could >  be thought of roughly as an "energy" (not free energy) this is certainly >  not a rigorous measure of model quality. Use an assessment function such >  as normalized DOPE for this purpose. >>   Let's say I want to make cutoff -100 for the objective function. In >>   which format it should be done? >> >>   automodel.max_molpdf  -100 >  Build your models, then assess them and pick the best ones. max_molpdf >  is designed as a filter to throw away the very worst models - it doesn't >  act on the final PDF, but the score of intermediate (partially >  optimized) models - the reasoning being to not waste time on trying to >  optimize a model that is very bad. Thus max_molpdf is not really what >  you want here. > >          Ben Webb, Modeller Caretaker > >  -- >  modeller-care@salilab.org             http://www.salilab.org/modeller/ >  Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage -------- Завершение пересылаемого сообщения --------