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