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IMP
2.3.0
The Integrative Modeling Platform
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IMP
2.3.0
The Integrative Modeling Platform
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Protocols for sampling structures and analyzing them. More...
Protocols for sampling structures and analyzing them.
Classes | |
| class | AnalysisReplicaExchange0 |
| A macro for running all the basic operations of analysis. More... | |
| class | BuildModel1 |
| this building scheme needs a data structure with the following fields comp_name hier_name color fasta_file fasta_id pdb_name chain_id res_range read_em_files bead_size rb super_rb em_num_components em_txt_file_name em_mrc_file_name More... | |
| class | ReplicaExchange0 |
| A macro to help setup and run replica exchange, supporting monte carlo and molecular dynamics. 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))]