pdbShapeFit
Usage
Usage: pdbShapeFit
Options:
[-i[nput]pdb[File] InPDB (NULL ).as(inFile ) ] :Essential :InputDataFile
[-i[nput]mrc[File] InMRC (NULL ).as(inFile ) ] :Essential :InputDataFile
[-C[ontour] Contour (0.0 ).as(Real ) ] :Essential :Contour
[-C[ontour]M[ode] ContourMode (0 ).as(Integer ) ] :Optional :ContourMode: refer to mrcImageContourSurfaceCreate
[-o[utput of ]mrc OutMRC (NULL ).as(outFile ) ] :Optional :OutputDataFile
[-o[utput of ]txt OutTxt (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)
[-P[DB]C[ontour]M[ode]surfaceMode (0 ).as(Integer ) ] :Optional :PDB SurfaceMode: refer to pdbSurface
[-order order (1.7 ).as(Real ) ] :Optional :order: refer to pdbSurface
[-refine refine (2 ).as(Integer ) ] :Optional :refine: refer to pdbSurface
[-size size (3 ).as(Integer ) ] :Optional :size: refer to pdbSurface
[-weight weight (100 ).as(Real ) ] :Optional :weight: refer to pdbSurface
[-mergin mergin (3.0 ).as(Real ) ] :Optional :mergin: refer to pdbSurface
[-thres thresHold (0.0 ).as(Real ) ] :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 ).as(inFile ) ] :Optional :ConfigurationFile
[-m[ode] mode (0 ).as(Integer ) ] :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.