Dear Modeller Caretaker,
I'm studying an homotetramer and i want to identify new sidechain orientations on a specific helix segment without any more changes in the protein structure of my initial pdb. So i tried the loopmodel routine:
################################################################### from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose() env = environ() env.io.atom_files_directory = ['.']
class MyLoop(loopmodel): def select_loop_atoms(self): return selection(self.residue_range('232:A', '268:A'), self.residue_range('232:B', '268:B'), self.residue_range('232:C', '268:C'), self.residue_range('232:D','268:D')).only_sidechain()
m = MyLoop(env, inimodel = 'herg_merged.pdb', # initial model sequence = 'herg_trg') # target
m.loop.starting_model= 1 # index of the first model m.loop.ending_model = 50 # index of the last model
m.loop.md_level = refine.very_fast
m.make() # do refinement ###########################################################
Therefore, I obtained 50 models with different sidechain-orientations over the specified segments. My question is the following:
?- Is it possible to preserve the symmetry of the sidechains over all the subunits? or...to perform a total symmetry of the models by a post-processing step of refinement?
Furthermore, I tried also to define special symmetry restraints, but all the 50 models resulted equals between them... it seems that nothing happens:
############################################
def special_restraints(self, aln): s1 = selection(self.chains['A']) s2 = selection(self.chains['B']) s3 = selection(self.chains['C']) s4 = selection(self.chains['D']) self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s1, s3, 1.0)) self.restraints.symmetry.append(symmetry(s1, s4, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0)
#################################################
Thank's in advance for your time and consideration
My regards, Giampaolo