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We provide a list of the possible parameter keywords for the inputfile (for details see section 2.2 of the usermanual):
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### BioEM posterior probability computation:
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- **PIXEL_SIZE** (float): Micrograph pixel size in ångström.
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- **NUMBER_PIXELS** (int): Assuming a square particle-image, it is the number of pixels along an axis. This should coincide with the number of pixels read from the micrograph.
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- **USE_QUATERNIONS:** (Integration of Orientations) If using quaternions to the describe the orientations. Recommended for uniformly sampling of SO3 with the quaternions lists available in the Quaternions directory.
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- **GRIDPOINTS_QUATERNION** (int): (Integration of Orientations) For a hypercubic grid quaternion sampling. Each quaternion is within [-1,1]. (int) is the number of grid points per dimension.
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- **GRIDPOINTS_QUATERNION** (int): (Integration of Orientations) For a hypercubic grid quaternion sampling. Each quaternion is within [-1,1]. (int) is the number of grid points per dimension.
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- **CTF_DEFOCUS** (float) (float) (int): (CTF Integration) Grid sampling of CTF defocus, Df . Units of micrometers. (float) (float) are the starting and ending limits, respectively, and (int) is the number of grid points.
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- **CTF_AMPLITUDE** (float) (float) (int): (CTF Integration) Grid sampling of the CTF amplitude, A (adimensional in [0,1]). (float) (float) are the starting and ending limits, respectively, and (int) is the number of grid points.
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- **DISPLACE_CENTER** (int) (int): (Integration of particle center displacement) Sampling within a square grid. Units of pixels. (int) (int) are the maximum displacement from the center in both directions, and the grid spacing, respectively. |
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- **DISPLACE_CENTER** (int) (int): (Integration of particle center displacement) Sampling within a square grid. Units of pixels. (int) (int) are the maximum displacement from the center in both directions, and the grid spacing, respectively.
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### Optional keywords
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- **ELECTRON_WAVELENGTH** (float): To change the default value of the electron wavelength (float) used to calculate the CTF phase with the defocus. Default 0.019688 °A.
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- **PRIOR_MODEL** (float): Prior probability of model. **Default** 1.
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- **PRIOR_ANGLES**: To read the prior of each orientation in the input file of orientations.
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- **SIGMA_PRIOR_B_CTF (float): To change the Gaussian width of the prior probability of the CTF envelope parameter b (section 2.2.5 of usermanua). **Default** 50 AA. |