====================================================================== ====================================================================== ==== PASS - Putative Active Sites with Spheres ====================== ============================================= G. Patrick Brady ======= ====================================================================== = 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) = ======================================================================