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)
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ID unfix x y z rootB radius
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ID connect ID length rootB
......