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====  PASS - Putative Active Sites with Spheres ======================
============================================= G. Patrick Brady =======
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= USAGE:  pass ProteinPDBfile                               =
=                                                                    =
=    where  include:                                        =
=                                                                    =
=        <-outdir directory_path> ... Specifies that output (i.e.    =
=                     visualization scripts, PDB files for probes,   =
=                     ASPs, ligands, etc) is to be sent to the       =
=                     specified directory path (defaults to the      =
=                     current directory, ./ )                        =
=        <-more>  ... Identify an enhanced set of probe spheres and  =
=                       active site points (ASPs)                    =
=        <-allprobes> ... Produce a display of all probe spheres     =
=                     (i.e. suppress smoothing which, by default,    =
=                     eliminates any probes that do not have at      =
=                     least smoothcount neighbors lying within       =
=                     smoothradius Angstroms).                       =
=        <-volumes> ...  Smooth the final probe spheres, group them  =
=                     via clustering, and compute the volumes of the =
=                     resulting regions.  Outputs several measures   =
=                     of nearness to ligands, in the event that some =
=                     are present.                                   =
=        <-noprobes>  ... Do NOT produce a PDB file of all final     =
=                     probe spheres (default is to make this file)   =
=        <-layers>  ... Produce a PDB file of each layer of probe    =
=                     spheres (by default these files are NOT made)  =
=        <-waters>  ... Treat waters as part of the protein (by      =
=                     default, waters are removed and ignored)       =
=        <-heavyonly> ... Exclude hydrogen atoms from calculation    =
=                     of probes. Default is to sense from input PDB  =
=        <-hydrogen> ... Include hydrogen atoms in probe calculation =
=        <-ligand PDBfilename>  ... Read-in a ligand from a          =
=                     separate PDB file (supercedes any HETATM       =
=                     ligand(s) in ProteinPDBfile)                   =
=  Visualization Script Files: load, color, and render the protein,  =
=              probe spheres, ASPs, and ligand(s).  In some cases    =
=              radial subsets centered on the ASPs are automatically =
=              defined.                                              =
=        <-cerius2> ... Produce a Cerius2 script (filename.log)      =
=        <-insightII> ... Produce an InsightII script (filename.bcl) =
=        <-moe> ... Produce a MOE script (filename.svl)              =
=        <-quanta> ... Produce a Quanta script (filename.rec)        =
=        <-rasmol> ... Produce a RasMol script (filename.ras)        =
=        <-sybyl> ... Produce a Sybyl script (filename.col)          =
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