# pdbShapeFit

## Usage

    Usage: pdbShapeFit
    Options:
        [-i[nput]pdb[File]   InPDB               (NULL      )] :Essential :InputDataFile
        [-i[nput]mrc[File]   InMRC               (NULL      )] :Essential :InputDataFile
        [-C[ontour]          Contour             (0.0       )] :Essential :Contour
        [-C[ontour]M[ode]    ContourMode         (0         )] :Optional  :ContourMode: refer to mrcImageContourSurfaceCreate
        [-o[utput of ]mrc    OutMRC              (NULL      )] :Optional  :OutputDataFile
        [-o[utput of ]txt    OutTxt              (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)
        [-P[DB]C[ontour]M[ode]surfaceMode         (0         )] :Optional  :PDB SurfaceMode: refer to pdbSurface
        [-order              order               (1.7       )] :Optional  :order: refer to pdbSurface
        [-refine             refine              (2         )] :Optional  :refine: refer to pdbSurface
        [-size               size                (3         )] :Optional  :size: refer to pdbSurface
        [-weight             weight              (100       )] :Optional  :weight: refer to pdbSurface
        [-mergin             mergin              (3.0       )] :Optional  :mergin: refer to pdbSurface
        [-thres              thresHold           (0.0       )] :Optional  :threshold: refer to pdbSurface
        [-I[nverse]          ] :Optional  :Black is High Density.
        [-Centre             ] :Optional  :Filament-axis is x=0, y=0
        [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
        [-m[ode]             mode                (0         )] :Optional  :Mode
    ----- Additional Usage -----
        -ipdb   : Filename : An atomic model to be fitted (PDB)
        -imrc   : Filename : 3-D density map (mrc-formated)
        -omrc   : Filename : fitting score map (MRC)
                             z=0: a max-score map of an phi-z plane which includes a max score point.
                                  The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
                             z=1: a max-score map of an psi-theta plane which includes a max score point.
                                  The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
                             z=2: a score map of an x-y plane which includes a max score point.
        -otxt   : Filename : fitting results (Text)
        -opdb   : Filename : An atomic model with a maximum score after fitting
        -x|y|zmin   : Initial value of z (should <= zmax)
        -x|y|zmax   : Final   value of z
        -x|y|zd     : Delta z for fitting (should !=0)
        -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
        -phi|psi|thetamax : Final value of phi  (should !=0)
        -phi|psi|thetad   : Delta phi for fitting (should >0)
        -C      : Contour level of map file
        -Inverse: Protein has high density on the image
        -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
        -EA     : Euler Angle Set : ZOYS: z -> y -> x
        -c      : Not used now
        -m   0 : Count the atom number inside the contour.