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IMP Reference Guide  2.10.1
The Integrative Modeling Platform
Edit on GitHub version 2.10.1
pmi/membrane.py
1 ## \example pmi/membrane.py
2 """
3 This script shows how to simulate an a protein using a
4 Membrane restraint. This example show 3 ideal helices
5 that have different segments inside the membrane
6 """
7 
8 import IMP
9 import IMP.atom
10 import IMP.rmf
11 import IMP.pmi
12 import IMP.pmi.topology
13 import IMP.pmi.dof
14 import IMP.pmi.macros
15 import IMP.pmi.restraints
16 import IMP.pmi.restraints.basic
17 import IMP.pmi.restraints.stereochemistry
18 import IMP.pmi.restraints.basic
19 import sys
20 
21 IMP.setup_from_argv(sys.argv,
22  "Simulation of a protein using a membrane restraint")
23 
24 model = IMP.Model()
25 s = IMP.pmi.topology.System(model)
26 st = s.create_state()
27 
28 # Create molecules and add helix representation
29 # this makes a c-alpha chain in approximately the shape of a helix
30 mols = []
31 
32 for i, len_helix in enumerate([20, 40, 80]):
33  mol = st.create_molecule(
34  "helix_%s" % (str(i)), sequence="A" * len_helix, chain_id="A"
35  )
36  mol.add_representation(mol, resolutions=[1], ideal_helix=True)
37  mols.append(mol)
38 hier = s.build()
39 
40 dof = IMP.pmi.dof.DegreesOfFreedom(model)
41 for mol in mols:
42  dof.create_rigid_body(mol,
43  max_trans=3.0,
44  max_rot=0.5)
45 ##############################
46 # Connectivity
47 ##############################
48 output_objects = []
49 sample_objects = []
50 rmf_restraints = []
51 
52 crs = []
53 for mol in mols:
54  cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(mol)
55  cr.set_label(mol.get_name())
56  cr.add_to_model()
57  output_objects.append(cr)
58  crs.append(cr)
59 
60 ##############################
61 # Excluded Volume
62 ##############################
63 evr1 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(
64  included_objects=mols, resolution=1
65 )
66 evr1.add_to_model()
67 evr1.set_weight(1.0)
68 output_objects.append(evr1)
69 
70 ##############################
71 # Membrane restraint
72 ##############################
73 
74 mr = IMP.pmi.restraints.basic.MembraneRestraint(
75  hier,
76  objects_inside=["helix_0", (1, 20, "helix_1"), (20, 40, "helix_2")],
77  objects_above=[(21, 40, "helix_1"), (1, 19, "helix_2")],
78  objects_below=[(41, 80, "helix_2")],
79  weight=10,
80 )
81 
82 mr.add_to_model()
83 output_objects.append(mr)
84 
85 # For visualization purposes
86 mr.create_membrane_density()
87 
88 ###########################
89 # External barrier
90 ###########################
91 eb = IMP.pmi.restraints.basic.ExternalBarrier(hierarchies=hier, radius=50)
92 eb.add_to_model()
93 
94 ##############################
95 # Shuffle
96 ##############################
97 IMP.pmi.tools.shuffle_configuration(hier, max_translation=300)
98 print(dof.get_movers())
99 
100 ##############################
101 # Sampling
102 ##############################
103 
104 frames = 10 if IMP.get_is_quick_test() else 2000
105 rex = IMP.pmi.macros.ReplicaExchange0(model,
106  root_hier=hier,
107  crosslink_restraints=rmf_restraints,
108  monte_carlo_sample_objects=dof.get_movers(),
109  replica_exchange_maximum_temperature=3.0,
110  global_output_directory="output/",
111  output_objects=output_objects,
112  monte_carlo_steps=10,
113  number_of_frames=frames,
114  number_of_best_scoring_models=0)
115 
116 rex.execute_macro()
117 exit()