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IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Sampling exhaustiveness protocol. More...
Sampling exhaustiveness protocol.
This module implements the sampling exhaustiveness test described in Viswanath et al, 2017. The protocol is primarily designed to work with models generated by the Integrative Modeling Platform (IMP) (and more specifically the IMP::pmi module), but could probably be adapted for other systems.
pyRMSD is needed. (This is a fork of the original pyRMSD - which is no longer maintained - to fix bugs and add Python 3 support.)
In the Sali lab, pyRMSD is already built, so can be used with module load python2/pyrmsd or module load python3/pyrmsd.
The protocol is typically run using the imp_sampcon command line tool:
imp_sampcon show_stat to show the available fields (e.g. scoring function terms, restraint satisfaction) in an IMP::pmi stat file.imp_sampcon select_good to select a subset of good-scoring models from a set of IMP::pmi trajectories.imp_sampcon plot_score to plot the score distributions of the selected models.imp_sampcon exhaust to analyze the selected models and determine whether sampling was exhaustive.For a full demonstration of the protocol, see its usage in IMP's actin modeling tutorial.
The protocol can also handle systems with ambiguity (equivalent proteins, e.g. multiple protein copies), where this information needs to be considered while calculating the RMSD between models. The RMSD between two protein models is the minimum RMSD over permutations of equivalent proteins.
For example, if a system has 2 copies of protein A and 1 copy of protein B, i.e. the proteins are A.0, A.1,B.0. The RMSD between any pair of models m0 and m1, is the minimum RMSD between RMSD[m0(A.0,A.1,B.0) , m1(A.0,A.1,B.1)] and RMSD[m0(A.0,A.1,B.1), m1(A.1,A.0,B.1]. Note that the copies of A in m1 were interchanged while calculating the second RMSD.
To implement this, pyRMSD takes an additional argument symm_groups which is a list of particle indices of equivalent particles. For the above case for instance, symm_groups has one symmetric group with the particle indices of A.0 and A.1. symm_groups=[[[A.0.b0,A.1.b0],[A.0.b1,A.1.b1],[A.0.b2,A.1.b2]..[A.0.bn,A.1.bn]]]. Here A.X.bi is the index of the i'th bead in protein A.X and the ith beads of the two protein copies are considered equivalent particles.
To generate this list of symmetric groups, one needs to pass an additional file with the ambiguity option to the master exhaust script. The file contains one line per symmetric group, and components of symmetric groups are separated by white space. See also the example in symminput.
Functions | |
| def | get_data_path |
| Return the full path to one of this module's data files. More... | |
| def | get_example_path |
| Return the full path to one of this module's example files. More... | |
| def | get_module_name |
| Return the fully-qualified name of this module. More... | |
| def | get_module_version |
| Return the version of this module, as a string. More... | |
| def IMP.sampcon.get_data_path | ( | fname | ) |
Return the full path to one of this module's data files.
Definition at line 17 of file sampcon/__init__.py.
| def IMP.sampcon.get_example_path | ( | fname | ) |
Return the full path to one of this module's example files.
Definition at line 22 of file sampcon/__init__.py.
| def IMP.sampcon.get_module_name | ( | ) |
Return the fully-qualified name of this module.
Definition at line 12 of file sampcon/__init__.py.
| def IMP.sampcon.get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 7 of file sampcon/__init__.py.