# pdbRhoFit

## Usage

    Usage: pdbRhoFit
    Options:
        [-i[nput]pdb[File]   InPdb               (NULL      )] :Essential :InputDataFile
        [-i[nput]mrc[File]   InMrc               (NULL      )] :Essential :InputDataFile
        [-o[utput of ]mrc    OutMrc              (NULL      )] :Essential :OutputDataFile
        [-o[utput of ]txt    OutTxt              (NULL      )] :Optional  :OutputDataFile
        [-o[utput of ]par    OutPar              (stdout    )] :Optional  :OutputDataFile
        [-o[utput of ]pdb    OutPDB              (NULL      )] :Optional  :OutputDataFile
        [-xmin               xmin                (0         )] :Optional  :xmin for fitting
        [-xmax               xmax                (0         )] :Optional  :xmax for fitting
        [-xd[elta]           xDelta              (1         )] :Optional  :delta x for fitting
        [-ymin               ymin                (0         )] :Optional  :ymin for fitting
        [-ymax               ymax                (0         )] :Optional  :ymax for fitting
        [-yd[elta]           yDelta              (1         )] :Optional  :delta y for fitting
        [-zmin               zmin                (0         )] :Optional  :zmin for fitting
        [-zmax               zmax                (82        )] :Optional  :zmax for fitting
        [-zd[elta]           zDelta              (1         )] :Optional  :delta z for fitting
        [-E[uler]A[ngle]     EulerAngle          (ZOYS      )] :Optional  :Euler Angle for three-angle
        [-phimin             phimin              (0         )] :Optional  :phimin for fitting(degree)
        [-phimax             phimax              (194       )] :Optional  :phimax for fitting(degree)
        [-phid[elta]         phiDelta            (2         )] :Optional  :delta phi for fitting(degree)
        [-psimin             psimin              (0         )] :Optional  :psimin for fitting(degree)
        [-psimax             psimax              (0         )] :Optional  :psimax for fitting(degree)
        [-psid[elta]         psiDelta            (2         )] :Optional  :delta psi for fitting(degree)
        [-thetamin           thetamin            (0         )] :Optional  :thetamin for fitting(degree)
        [-thetamax           thetamax            (0         )] :Optional  :thetamax for fitting(degree)
        [-thetad[elta]       thetaDelta          (2         )] :Optional  :delta theta for fitting(degree)
        [-n[ormalize]w[eight]normalizeWeight     (100000000.0)] :Optional  :weight for normalize
        [-n[ormalize]C[ontour]normalizeContour    (0.0       )] :Optional  :Contour Level for Normalize
        [-I[nverse]          ] :Optional  :Black is High Density.
        [-Zminus             ] :Optional  :Shift to -z
        [-Tfactor            ] :Optional  :Consider T factor
        [-T[ factor ]lim[it] Tlim                (60        )] :Optional  :The atom will be neglected
        [-Centre             ] :Optional  :Filament-axis is x=0, y=0
        [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         )] :Optional  :Mode
        [-C[ontour]          contourLevel        (0.0       )... ] :Variable  :ContourLevel

    Usage of pdbRhoFit:
        -ipdb   : Filename of pdb file of atomic model
        -imrc   : Filename of mrc file of contour map
        -omrc   : Filename of mrc file of fitting results
        -otxt   : Filename of text file of fitting results
        -opar   : Filename of text file of fitting results
        -opdb   : Filename of pdb file with a max score after fitting results
        -zmin   : Initial value of z (should <= zmax)
        -zmax   : Final value of z
        -zd     : Delta z for fitting (should >0)
        -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
        -phimax : Final value of phi (should >0)
        -phid   : Delta phi for fitting (should >0)
        -C      : Contour level (variable and MUST be last option)
        -Inverse: Protein has high density on the image
        -Zminus : Atomic model shift to -z while fitting
        -Tfactor: Consider temperature factor
        -Tlim   : The atoms whose T factor is above Tlim will be neglected
        -Centre : Filament-axis is x=0, y=0
        -c      : Not used now
        -m   0 : Count the atom number inside the contour.
             1 : Add the densities of atoms.