energyTransferModelCheck

Usage

Usage: energyTransferModelCheck
Options:
    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
    [-p[db]              PDB                 (NULL      )] :Optional  :Excluded Area by PDB: Input[PDB]
    [-P[dbs]             PDBs                (NULL      )] :Optional  :Excluded Area by PDB: Input[PDBFileList]
    [-P[DBs]W[ithInfo]   ] :Optional  :PDBFileList With Info: filename sigma[A]
    [-sigma              sigma               (1.0       )] :Optional  :SigmaOfAtom for All: sigma [pixel]x delta[A/pixel]
    [-sigmaA             sigmaA              (1.0       )] :Optional  :SigmaOfAtom for All: sigma [A]
    [-mrc                MRC                 (NULL      )] :Optional  :Excluded Area by mrc: Input[MRC]
    [-MRC                MRCs                (NULL      )] :Optional  :Excluded Area by MRC: Input[MRCFileList]
    [-MRCW[ithInfo]      ] :Optional  :MRCFileList with Info: filename contour near[A]
    [-C[ontour]          EContour            (10.       )] :Optional  :ContourLevel for Exclusion: Density 0
    [-Near               ENear               (1.        )] :Optional  :Near [pixel]: Exclusion Area: near[pixel] x delta [A/pixel]
    [-NearA              ENearA              (1.        )] :Optional  :Near [A]: Exclusion Area: near [A]
    [-r[estrict]         Rest                (NULL      )] :Optional  :Restricted Area: Input[mrc]
    [-R[estrict]         Rests               (NULL      )] :Optional  :Restricted Area: InputDataFileList[mrcs]
    [-contour            Contour             (10.       )] :Optional  :ContourLevel for Restriction
    [-near               Near                (1.        )] :Optional  :Near [pixel]: Restriction Area: near[pixel] x delta [A/pixel]
    [-nearA              NearA               (1.        )] :Optional  :Near [A]: Restriction Area: near[A] 
    [-R[estrictWithInfo] ] :Optional  :WithInfo: filename contour near[A]
    [-r[estrict]P        RestP               (NULL      )] :Optional  :Restricted Area: InputDataFile[pdb]
    [-R[estrict]P        RestsP              (NULL      )] :Optional  :Restricted Area: InputDataFileList[pdbs]: format: filename near[pixel]
    [-sigmaP             SigmaP              (1.        )] :Optional  :Sigma[pixel]: Restriction Area: sigma x delta [A]
    [-sigmaPA            SigmaPA             (1.        )] :Optional  :Sigma[A]: Restriction Area: sigma [A]
    [-nearP              NearP               (1.        )] :Optional  :Near [pixel]: Restriction Area: near x delta [A]
    [-nearPA             NearPA              (1.        )] :Optional  :Near [A]: Restriction Area: near [A]
    [-R[estrict]PW       ] :Optional  :WithInfo: filename near[A] sigma[A]
    [-delta              deltax              (5         )deltay              (5         )deltaz              (5         )] :Optional  :delta [A]
    [-sdelta             sdeltax             (5         )sdeltay             (5         )sdeltaz             (5         )] :Optional  :starting delta [A]
    [-start              startx              (5         )starty              (5         )startz              (5         )] :Optional  :start [A]
    [-end                endx                (5         )endy                (5         )endz                (5         )] :Optional  :end [A]
    [-maxIter            maxIter             (1         )] :Optional  :Max Iteration 
    [-startIter          startIter           (0         )] :Optional  :Start Iteration 
    [-neglect            neglect             (1e-4      )] :Optional  :neglect: probability for each term: not final probability
    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
    [-m[ode]             mode                (0         )] :Optional  :Mode
----- Additional Usage -----
----- Point Information : Each ID has no space character. -----
ID fix     x y z rootB radius(noUse)
......
ID unfix   x y z rootB radius
......
ID connect ID length rootB
......