calcPSol
Compute the solvent PRE given a molecule structure and a restraint list.
Usage: calcPSol [option] -table <solvent PRE table> <pdb files>
Options:
-psf <psf filename> - specify a psf filename. If omitted PSF info is
automatically generated from the pdb file.
-showRestraints - print out all back-calculated solvent PRE values
to the terminal.
-selection <atom sel> - atom selection string used to in defining the
molecular surface. By default all read atoms are
used.
-probeR <val> - specify probe radius [5.400]
-radiusOffset <val> - specify value to be added to all atomic
radii [same as probeR]
-rmin <val> - specify minimum distance from nucleus to the
surface describing the excluded volume [0.100]
-centerOffset <val> - center offset of solute - for off-center
paramagnetic center [0]
-noFitConc - dont' adjust the concentration rho0 to optimize
the fit to experiment.
-prefactor <val> - Specify the prefactor k in the expression for
solvent PRE:
\Gamma_2 = k \int_{V_e} dv 1/r^6,
where \Gamma_2 is the sPRE value,
r is the distance of the measured
nucleus to a point in the solvent, and the
integral is over all space excluding the
PRE-cosolute-excluded region.
This implies -noFitConc behavior, as the
calculated values will no longer depend on
rho0.
-addMissingAtoms - Adds missing atomic coordinates in the genSel
atom selection. These atoms are added only if
there is an existing atom to which they are
bound.
-singleEns - Treat the files specified as an ensemble instead
of a set of individual structures.
-ensWeights <vals> - a colon-separated list of weights to use on
structure ensemble members. If not specified, the
ensemble members are weighted equally.
-optEnsWeights - If specified, the ensemble populations will be
optimized to fit the experimental solvent PREs.
-targetType <spec> - The energy term used for ensemble population
optimization- can be "gamma" or "correlation"
["gamma"]
-residTable - allow an input table where each line takes the
format:
RESID OBS ERR
In this case, each restraint atom selection
becomes the intersection of the -genSel argument
and "resid RESID".
-genSel - selection used to generate dummy restraints if
the table is specified as "generate" ["name HN"], o
or -residTable is specified.
-genPDB - write a PDB file named psol.pdb which has the
calculated sPREs in the occupancies column and the
observed values in the b-factor column.
-genSurface - generate a molecular surface describing the
surface-excluded volume to be loaded in VMD
TCL commands.
-plot - produce a plot of calculated vs. observed
solvent PREs. Error bars indicate input experimental
errors and the spread between calculated
structures' rdcs.
-plotVsResid - produce a plot of calculated and observed
couplings as a function of residue number.
Error bars indicate input experimental
errors and the spread between calculated
structures' sPREs.
If the string "generate" is given as the table name, dummy restraints are generated from the -genSel argument, so that no input table is required. Specific MODEL records within a pdb file can be chosen using the syntax file.pdb:2 where the integer following the colon specifies the MODEL record. A range of MODELs can be chosen using a model specifier BEG-END, where BEG and END specify start and end record numbers, respecitvely.