Validation

Validation of your results

Calculate a Fourier Shell Correlation (FSC) curve using fsc.py

After aligning the subtomograms one wants to know the quality/resolution of the subtomogram average. The resolution of a model is typically determined from the FSC curve, calculated using two so-called half-maps (model from the odd particles vs model from the even particles). To this end you can use the following command:

pytom PathToPyTom/bin/fsc.py --v1 your3DModel-Odd.em --v2 your3DModel-Even.em --fsc yourFSCCriterion --mask yourMask.em --pixelsize yourPixelSize --plot

This will generate an average of yourParticleListXML called pathOfAverage.em. Here are the possible parameters:

NAME
    fsc.py
DESCRIPTION
    Determine resolution by FSC.
OPTIONS
    --v1    First volume path. (Is optional: Yes; Requires arguments: Yes)
    --v2    Second volume path. (Is optional: Yes; Requires arguments: Yes)
    --pl    A particleList if v1 and v2 are not available. (Is optional: Yes; Requires arguments: Yes)
    --fsc    The FSC criterion. Value between 0.0 and 1.0. Standard values are 0.5 or 0.3 (Is optional: No; Requires arguments: Yes)
    --numberBands    Number of bands (optional). If not set, numberBands = cubesize/4. (Is optional: Yes; Requires arguments: Yes)
    -m, --mask    Mask (optional, but recomended). (Is optional: Yes; Requires arguments: Yes)
    --pixelsize    Pixelsize in Angstrom (optional). Will return resolution in Angstrom.  (Is optional: No; Requires arguments: Yes)
    --xml    Output in XML. (optional)  (Is optional: Yes; Requires arguments: No)
    --randomizePhases    Correlation threshold beyond which phases are randomized. Default None. (optional)  (Is optional: Yes; Requires arguments: Yes)
    --plot    Plot Output. (optional)  (Is optional: Yes; Requires arguments: No)
    --outputFolder    Output Folder. (optional)  (Is optional: Yes; Requires arguments: Yes)
    --combinedResolution    Calculate the resolution for two volumes combined. (Is optional: Yes; Requires arguments: No)
    -v, --verbose    Verbose data. (optional)  (Is optional: Yes; Requires arguments: No)
    -g, --gpuID    Which gpu do you want to use? (Is optional: Yes; Requires arguments: Yes)
    -h, --help    Help. (Is optional: Yes; Requires arguments: No)
AUTHORS
    Thomas Hrabe