rexanalysis.pl

Usage

usage:   rexanalysis.pl [options]
options: [-dir workdir]
         [-inx from:to] [-step value]
         [-byclient clientid]
         [-bytemp temp]
         [-bycond condindex]
         [-order client|temp]
         [-apply cmd]
         [-function file]
         [-nanvalue value]
         [-wham prop:fname:from:to:nbins[=...]]
         [-whamtemp temp[:temp2...]
         [-whamener file]
         [-out dcdfile]
         [-atoms from:to]  [-nsel Selection]
         [-verbose]

Show source

Options

-help 

usage information

Examples

rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A | centerOfMass.pl " > centerOfMass-A-temp310.data
This command computes the center of mass for a series of pdb files, based on temperature from replica exchange simulations. Note how multiple MMTSB toolset commands are invoked in this one line.

 add output

The data in the output file can be pulled out by:
awk '{print $5,$6,$7}' centerOfMass-A-temp310.data > centerOfMass-A-temp310.data.dat

rexanalysis.pl -inx 1500:2000 -best -apply "convpdb.pl -chain A | centerOfMass.pl " > centerOfMass-A-cond0.data
This command computes the center of mass for a series of pdb files, based on first condition from replica exchange simulations ("-best" is the shortcut for "-bycond 0" and usually corresponds to the lowest temperature).

 add output

rexanalysis.pl -inx 1500:2000 -bycond 2 -apply "convpdb.pl -chain B | rgyr.pl " > rgyr-cond2-B.data
This command computes the radius of gyration for a series of pdb files, based on condition 2 from replica exchange simulations.

 add output

The data in the output file can be pulled out by:
awk '{print $5}' rgyr-cond2-B.data >rgyr-cond2-B.data.dat