pdbRhoFitTm
Usage
Usage: pdbRhoFitTm
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
[-Sx Sx (50 )] :Essential :x of rotation axis
[-Sy Sy (110 )] :Essential :y of rotation axis
[-Sz Sz (110 )] :Essential :z of rotation axis
[-o[utput of ]txt OutTxt (NULL )] :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 pdbRhoFitTm:
-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
-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
-Sx : x of rotation axis
-Sy : y of rotation axis
-Sz : z of rotation axis
-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.