[modeller_usage] Fwd: automodel.max_molpdf recommended values and usage format

[Andrew Voronkov <>]

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" <>:

>  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
>
>  --
>               http://www.salilab.org/modeller/
>  Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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