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.

Additional common options