IMP.pmi.macros Namespace Reference

Protocols for sampling structures and analyzing them. More...

Detailed Description

Protocols for sampling structures and analyzing them.

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...
class	ReplicaExchange0
	A macro to help setup and run replica exchange. More...

Functions
def	BuildModel0
	Construct a component for each subunit (no splitting, nothing fancy). More...

Function Documentation

def IMP.pmi.macros.BuildModel0	(		m,
			data,
			resolutions = [1,
			missing_bead_size = 20,
			residue_per_gaussian = None
	)

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))]

Note

This function is only available in Python.

Definition at line 394 of file macros.py.