IMP
2.3.1
The Integrative Modeling Platform

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 multistate 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 topscoring 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 , 

missing_bead_size = 20 , 

residue_per_gaussian = None 

) 
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))]