llExtractWithLayerSeparation
From EosPedia
llExtractWithLayerSeparation is Eos's Command.
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Essential | Input: mrcImage(FFT) | NULL |
| -I | Optional | Input: llData(Already separated): (InLLNea, InLLFar) | (NULL, NULL) |
| -r | Optional | Reference: llData(Gnl(R) Space) | NULL |
| -o | Essential | Output: llData(Average File) | NULL |
| -o2 | Optional | OutputList: llData(Each Filament which has the same orientation as average) | NULL |
| -o3 | Optional | OutputList: llData(Difference of each filament) | NULL |
| -o4 | Optional | OutputList: llData(Each Filament which has the same orientaion as original filament) | NULL |
| -o5 | Optional | OutputList: llData(P-Value) | NULL |
| -o6 | Optional | OutputList: llData(Q-Value) | NULL |
| -o7 | Optional | Output: ASCII(Two subsets for resolution estimation) | NULL |
| -o8 | Optional | Output: ASCII(For Back Projection) | NULL |
| -o9 | Optional | OutputList: ASCII(x shift, z shift and dY information) | NULL |
| -comment | Optional | Comment | NULL |
| -symmetry | Optional | Symmetry for back projection text file | 1.0 |
| -l | Essential | LayerLineInformation | NULL |
| -lfinal | Optional | LayerLineInformation(Final) | NULL |
| -li | Optional | LayerLineInformationImportant | NULL |
| -liw | Optional | Weight of Important Layer | 1.0 |
| -liwStart | Optional | Weight of Important Layer | 1.0 |
| -liwStep/td> | Optional | Weight of Important Layer | 1.0 |
| -la | Optional | LayerLineInformationForAxisSearch | NULL |
| -law | Optional | Weight of Important Layer for AS | 1.0 |
| -lawStart | Optional | Weight of Important Layer for AS | 1.0 |
| -lawStep | Optional | Weight of Important Layer for AS | 1.0 |
| -truePitch | Essential | true pitch [A] | 430.0 |
| -rMax | Essential | rMax [A] | 100.0 |
| -rMaxMin | Optional | rMaxMin [A] | 100.0 |
| -RMax | Optional | RMax [/A] | 0.1 |
| -RMaxFirst | Optional | RMaxFirst [/A] (Def: RMax) | 0.04 |
| -RMaxStep | Optional | RMaxStep [/A] | 0.02 |
| -RRMax | Optional | Radial RMax [/A] | 0.1 |
| -RRMaxFirst | Optional | Radial RMaxFirst [/A] (Def: RMax) | 0.04 |
| -RRMaxStep | Optional | Radial RMaxStep [/A] | 0.02 |
| -delBR | Optional | delBR [/A] | 0.0002 |
| -rms | Optional | rms | 1e-6 |
| -narrowSearch | Optional | narrowSearch [Degree]: P-value and Q-value | 1.0 |
| -nextTimes | Optional | nextTimes: rms | 1e-4 |
| -maxIter | Optional | max Iteration | 10 |
| -maxIter2 | Optional | max Iteration on the same RMax and RRMax | 1 |
| -maxIter3 | Optional | max Iteration on the same RMax, RRMax, and Weight | 1 |
| -lambda | Optional | lambda | 1.0 |
| -ctf | Optional | CTF Compensation | 0 |
| -WhiteNoise | Optional | White Noise | 0.0 |
| -below | Optional | below | 90.0 |
| -noantipole | Optional | No Antipole | |
| -magLimit | Optional | magLimit | |
| -eachTime | Optional | each time | |
| -continue | Optional | continue | NULL |
| -forContinue | Optional | For continue | NULL |
| -phi | Optional | phi [degree]: (phimin, phimax, delphi)) | (0.0, 360.0, 10.0) |
| -z | Optional | z [A]: (zmin, zmax, delz) | (0.0, 30.0, 5.0) |
| -shift | Optional | shift [A]: (shiftmin, shiftmax, delshift) | (-10.0, 10.0, 1.0) |
| -log | Optional | Logfile | stdout |
| -Normalization | Optional | Normalization | |
| -pvm | Optional | pvmNumber | 0 |
| -pvmList | Optional | pvmList | NULL |
| -pvmServer | Optional | Work as a server | |
| -pvmClient | Optional | Work as a client | |
| -wd | Optional | Working Directory | ./ |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 0 |
| -h | Optional | Help |
If -ctf, the file list indicated by -i must include the below information filename weight defocus[A] Cs[mm] AccV[kV] ratioOfAmpToPhase mode
>> llDataSepartionControlFile << llMax(different) nl Z numberOfN n0 n1 n2...
-m details
| Value | Description |
|---|---|
| 0 | The 1st version algorism(Sharing) |
| 1 | The 2nd version algorism(Least Square) |
-ctf details
| Value | Description |
|---|---|
| 0 | |CTFi|/Sigma(SQR(CTFi)) |
| 1 | CTFi /Sigma(SQR(CTFi)) |
