[modeller_usage] Refinement step questions

Dear MODELLER users!

 I am currently doing a homology modeling project, in which salt bridges are important. Therefore I want to make the most out of the refinement protocol (of course I will do some final refinement with other softwares), especially with molecular dynamics. I intend to use and slightly modify the automodel protocols, but I ran into some problems because of my limited python knowledge. My two questions are: the molecular dynamics refinement returns the final structure from each simulation, but I want it to return the ones with minimal energy (md_return='MINIMAL'), how could I specify it in my script while still using the standard automodel protocols (e.g. with md_level = refine.slow). My other question is that how could I also specify in my script to create a CHARMM trajectory of the automodel MD refinement steps(I tried it with automodel.get_refine_actions(), but I failed to define it properly because of my mentioned lack of python knowledge)?

Thank you for your help in advance!

 Best regards,

 Gergely Banoczi

 My script is:

MODELING SCRIPT

from modeller import *

from modeller.automodel import *   

from modeller.parallel import *

from mymodel import mymodel

j = job()

j.append(local_slave())

j.append(local_slave())

j.append(local_slave())

j.append(local_slave())

j.append(local_slave())

j.append(local_slave())

j.append(local_slave())

j.append(local_slave())

log.very_verbose()

env = environ()

env.io.atom_files_directory = ['.', '../atom_files']

env.io.hetatm = True

env.io.water = True

a = mymodel(env,deviation=0,

            alnfile  = 'xyz.ali' ,   

            knowns   = ('xyz','zxy') ,

            sequence = 'PcPAL', assess_methods=(assess.DOPE, assess.GA341))      

 

a.starting_model= 1                

a.ending_model  = 8

a.md_level = refine.slow

                                  

a.use_parallel_job(j)

a.make()

CLASS DEFINING SCRIPT

from modeller import *

from modeller.automodel import *   

class mymodel(automodel):

def special_patches(self, aln):

         self.rename_segments(segment_ids=['A', 'B', 'C', 'D'], renumber_residues=[25, 25, 25, 25])

        def special_restraints(self, aln):

rsr = self.restraints

at = self.atoms

s1 = selection(self.chains['A']).only_atom_types('CA')

s2 = selection(self.chains['B']).only_atom_types('CA')

s3 = selection(self.chains['C']).only_atom_types('CA')

s4 = selection(self.chains['D']).only_atom_types('CA')

rsr.symmetry.append(symmetry(s1, s2, 1.0))

rsr.symmetry.append(symmetry(s2, s3, 1.0))

rsr.symmetry.append(symmetry(s3, s4, 1.0))

def user_after_single_model(self): self.restraints.symmetry.report(1.0)