IMP Manual
for IMP version 2.8.0
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With the system representation built and data restraints entered, the system is now ready to sample configurations. A replica exchange run can be set up using the ReplicaExchange0 macro:
See the ReplicaExchange0 documentation for a full description of all of the input parameters.
The sampling is performed by executing the macro built above:
The script generates an output
directory containing the following:
pdbs
: a directory containing the 100 best-scoring models (see the number_of_best_scoring_models
variable above) from the run, in PDB format.rmfs
: a single RMF file containing all the frames. RMF is a file format specially designed to store coarse-grained, multi-resolution and multi-state models such as those generated by IMP. It is a compact binary format and (as in this case) can also be used to store multiple models or trajectories.stat.*.out
. This file contains information on each restraint, MC acceptance criteria and other things at each step.Gathering Data from statfile Data from the stat file can be parsed and analyzed using two utilities:
process_output.py
- parses the statfile and returns columns of interestplot_stat.sh
- plots one or two columns of data (requires gnuplot)process_output.py
usage:
plot_stat.sh
usage:
Analysis of the sampled models is described in Stage 4 - Analysis Part 1.