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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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- **GRIDPOINTS_ALPHA** (int): (Integration of Orientations) Number of grid points used in the integration over Euler angle alpha in [-pi,pi]. Here a cubic grid in Euler angle space is performed. The integral over Euler angle gamma is identical to that of alpha.
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- **GRIDPOINTS_BETA** (int): (Integration of Orientations) Number of grid points used in the integration over cos(beta) in [-1,1].
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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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- **CTF_DEFOCUS** (float) (float) (int): (CTF Integration) Grid sampling of CTF defocus, Df . Units of micrometers.
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(float) (float) are the starting and ending limits, respectively, and (int) is the number of grid points.
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CTF B ENV (float) (float) (int): (CTF Integration) Grid sampling of envelope parameter b. Units of °A2. (float)
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(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
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2 [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
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pixels. (int) (int) are the maximum displacement from the center in both directions, and the grid spacing, respectively. |
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