3 This script shows how to simulate residue-protein
4 binding contacts inferred from mutagenesis studies.
5 This example shows protein A binding to protein B
6 through a set of residues predicted to be required
7 for binding in mutagensis studies.
10 from __future__
import print_function
27 print(
"This example is too slow to test in debug mode - run without")
28 print(
"internal tests enabled, or without the --run-quick-test flag")
32 |molecule_name|color|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rigid_body|super_rigid_body|chain_of_super_rigid_bodies|
33 |Rpb4 |red |1WCM.fasta |1WCM:D |1WCM_fitted.pdb |D|1,END |0 |5|0 |1 | | ||
34 |Rpb7 |gold |1WCM.fasta |1WCM:G |1WCM_fitted.pdb |G|1,END |0 |5|0 |2 | | ||
39 tf = tempfile.NamedTemporaryFile(delete=
False, mode=
'w')
55 hier, dof = bs.execute_macro()
64 moldict = bs.get_molecules()[0]
66 for molname
in moldict:
67 for mol
in moldict[molname]:
70 output_objects.append(cr)
76 included_objects=mols)
78 output_objects.append(evr)
87 hier, selection=(
'Rpb7', 38, 44,
'Rpb4'), label=
'B38_44')
91 output_objects.append(br)
99 molecule=
"Rpb4").get_selected_particles()
101 xyzs, rbs = dof.disable_movers(part_p1,
109 dof.optimize_flexible_beads(100)
114 monte_carlo_sample_objects=dof.get_movers(),
115 global_output_directory=
'output/',
116 output_objects=output_objects,
117 monte_carlo_steps=10,
118 number_of_best_scoring_models=0,
119 number_of_frames=500)