pdbRhoFit

Usage

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