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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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Protocols for sampling structures and analyzing them. More...
Protocols for sampling structures and analyzing them.
A macro to help setup and run replica exchange. Supports monte carlo and molecular dynamics. Produces trajectory RMF files, best PDB structures, and output stat files.
| model | The IMP model |
| representation | PMI.Representation() (or list of them, for multi-state modeling) |
| root_hier | Instead of passing Representation, just pass a hierarchy |
| mote_carlo_sample_objcts | Objects for MC sampling |
| molecular_dynamics_sample_objects | Objects for MD sampling |
| output_objects | Objects with get_output() for packing into stat files |
| crosslink_restraints | Harmonic restraints to go in output RMF files |
| monte_carlo_temperature | MC temp |
| replica_exchange_minimum_temperature | Low temp for REX |
| replica_exchange_maximum_temperature | High temp for REX |
| num_sample_rounds | Number of rounds of MC/MD per cycle |
| number_of_best_scoring_models | Number of top-scoring PDB models to keep around |
| monte_carlo_steps | Number of MC steps per round |
| molecular_dynamics_steps | Number of MD steps per round |
| number_of_frames | Number of REX frames to run |
| nframes_write_coordinates | How often to write the coordinates of a frame |
| write_initial_rmf | Write the initial configuration |
Classes | |
| class | AnalysisReplicaExchange0 |
| A macro for running all the basic operations of analysis. More... | |
| class | BuildModel |
| A macro to build a Representation based on a Topology and lists of movers. More... | |
| class | BuildModel1 |
| Deprecated building macro - use BuildModel() More... | |
Functions | |
| def | BuildModel0 |
| The macro construct a component for each subunit (no splitting, nothing fancy) You can pass the resolutions and the bead size for the missing residue regions. More... | |
| def IMP.pmi.macros.BuildModel0 | ( | m, | |
| data, | |||
resolutions = [1, |
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missing_bead_size = 20, |
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residue_per_gaussian = None |
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| ) |
The macro construct a component for each subunit (no splitting, nothing fancy) You can pass the resolutions and the bead size for the missing residue regions.
To use this macro, you must provide the following data structure:
Component pdbfile chainid rgb color fastafile sequence id in fastafile
data = [("Rpb1", pdbfile, "A", 0.00000000, (fastafile, 0)), ("Rpb2", pdbfile, "B", 0.09090909, (fastafile, 1)), ("Rpb3", pdbfile, "C", 0.18181818, (fastafile, 2)), ("Rpb4", pdbfile, "D", 0.27272727, (fastafile, 3)), ("Rpb5", pdbfile, "E", 0.36363636, (fastafile, 4)), ("Rpb6", pdbfile, "F", 0.45454545, (fastafile, 5)), ("Rpb7", pdbfile, "G", 0.54545455, (fastafile, 6)), ("Rpb8", pdbfile, "H", 0.63636364, (fastafile, 7)), ("Rpb9", pdbfile, "I", 0.72727273, (fastafile, 8)), ("Rpb10", pdbfile, "L", 0.81818182, (fastafile, 9)), ("Rpb11", pdbfile, "J", 0.90909091, (fastafile, 10)), ("Rpb12", pdbfile, "K", 1.00000000, (fastafile, 11))]