mrc2Dto3D

Usage

Usage: mrc2Dto3D
Options:
    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Optional  :InputDataFile
    [-I[nput]            In2                 (NULL      ).as(inFileListNoOpen    ) ] :Optional  :InputDataFile
    [-each                                                                         ] :Optional  :Read each projection file if necessary, not at once.
    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
    [-O[utput]           Out2                (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile[2DMulti]
    [-Rmax               Rmax                (1.0       ).as(Real                ) ] :Optional  :Rmax: High Cut [/A]
    [-single             single              (1         ).as(Integer             ) ] :Optional  :SingleTiltMode
    [-singleFilter       singleFilter        (0         ).as(Integer             ) ] :Optional  :SingleFilterMode
    [-InterpolationMode  InterpolationMode   (1         ).as(Integer             ) ] :Optional  :InterpolationMode
    [-Double                                                                       ] :Optional  :DoubleTiltMode
    [-DoubleCounter      DoubleCounter       (NULL      ).as(outFile             ) ] :Optional  :DoubleCounter
    [-CounterThreshold   CounterThreshold    (1e-6      ).as(Real                ) ] :Optional  :CounterThreshold
    [-CounterThresholdModeCounterThresholdMode(0         ).as(Integer             ) ] :Optional  :CounterThresholdMode
    [-WeightMode         WeightMode          (0         ).as(Integer             ) ] :Optional  :WeightMode
    [-thicknessWeight                                                              ] :Optional  :ThicknessWeight
    [-Sub[Sampling]      SubSampling         (1         ).as(Integer             ) ] :Optional  :SubSampling: [pixel]
    [-PlusXrot                                                                     ] :Optional  :plus x-rotation by 180 for rasmol.
    [-N                  Nx                  (0         ).as(Integer             ) 
                         Ny                  (0         ).as(Integer             ) 
                         Nz                  (0         ).as(Integer             ) ] :Optional  :OutputSize
    [-SIRT                                                                         ] :Optional  :by SIRT
    [-max[Iter]          maxIter             (30        ).as(Integer             ) ] :Optional  :MaxIteration for SIRT
    [-rms                rms                 (1.0       ).as(Real                ) ] :Optional  :Ending Conditions: rms for SIRT
    [-CTF[Info]          CTFInfo             (NULL      ).as(inFileList          ) ] :Optional  :CTFInfo: for SIRT
    [-pthread            pthreadMax          (1         ).as(Integer             ) ] :Optional  :pthread: max
    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
----- Additional Usage -----
-m Option
    0:SimpleBackProjection
    1:FilteredBackProjection(Fourier Space)
    2:WeightedBackProjection(Real Space)
-single 0|1 
    0: tilt axis is parallel to x-axis
    1: tilt axis is parallel to y-axis
-singleFilter 0|1|2 
    0: simple rho filter
    1: Ram-Lak Filter
    2: Shepp-Logan Filter
-Double 
    Double Tilt 
-WeightMode 
    1 : RealSpace: Circle(same density)
    2 : RealSpace: Circle(weighted density)
    3 : RealSpace: Square(weighted density) 
    4 : Fourier Space : Plane(same density) -CounterThreshold 0.5
    5 : Fourier Space : Plane(Linear Gradient)-CounterThreshold 0.5
    6 : Fourier Space : Plane(Cosine Gradient) Current Recommende using -CounterThreshold 0.5
-------------------------------
-I Option file format
filename0 RotationOrder0 rot1 rot2 rot3
filename1 RotationOrder1 rot1 rot2 rot3
.......................................
>>> RotationOrder : Eular Angle Expression <<< 
Example: YOYS : RotY(rot3)RotX(rot2)RotY(rot1)*v
First Rotation  : y-axis : Y: Y     : [X|Y|Z] Axis used initially
Second Rotation : x-axis : O: Odd   : [O|E]   Parity of axis permutation
Last Rotation   : z-axis : Y: Yes   : [Y|N]   Repetition of initial axis as last
v1 = A v0                : S: Staic : [S|R]   Frame from which axes are taken