Restraints on pseudo atoms: Difference between revisions
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pseudo.py demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 9v1 or later. You will also need the [[attachment:pseudo.atm]] input. | pseudo.py demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 9v1 or later. You will also need the [[attachment:pseudo.atm]] input. | ||
Revision as of 01:51, 4 June 2008
pseudo.py demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 9v1 or later. You will also need the attachment:pseudo.atm input.
#!python from modeller import * from modeller.optimizers import conjugate_gradients e = environ() e.edat.dynamic_sphere = False log.verbose() # Read in a dummy PDB, which defines five real atoms - four are positioned at # the corners of a square in the xy place, and the fifth is off in space m = model(e, file='pseudo.atm') # Define a pseudo atom as the gravity center of the first 4 atoms, and add # it to the model's restraints p = pseudo_atom.gravity_center(m.atoms[0:5]) m.restraints.pseudo_atoms.append(p) # Create a restraint on the distance between the real fifth atom and the newly # created pseudo atom, and add it to the model's restraints. Since the mean is # zero, this will force atom 5 to coexist with the gravity center. r = forms.gaussian(group=physical.xy_distance, feature=features.distance(m.atoms[4], p), mean=0.0, stdev=0.100) m.restraints.add(r) # Calculate the starting energy of all atoms in the system, then optimize s = selection(m) s.energy() cg = conjugate_gradients() cg.optimize(s, max_iterations=200) # Write out the final coordinates m.write(file='pseudoout.atm')
It is straightforward to add restraints of this type to a comparative
modeling run - see for example, Adding additional restraints to the defaults.