MCore
MCore
MCore 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MCore
--port (Default: 14300) Port to use for REST API calls,
set to -1 to disable
--devicelist Space-separated list of GPU IDs to use for
processing. Default: all GPUs in the system
--perdevice_preprocess Number of processes per GPU used for map
pre-processing; leave blank = default to
--perdevice_refine value
--perdevice_refine (Default: 1) Number of processes per GPU used
for refinement; set to >1 to improve utilization
if your GPUs have enough memory
--perdevice_postprocess Number of processes per GPU used for map
pre-processing; leave blank = default to
--perdevice_refine value
--workers_preprocess List of remote workers to be used instead of
locally spawned processes for map
pre-processing. Formatted as hostname:port,
separated by spaces
--workers_refine List of remote workers to be used instead of
locally spawned processes for refinement.
Formatted as hostname:port, separated by spaces
--workers_postprocess List of remote workers to be used instead of
locally spawned processes for map
post-processing. Formatted as hostname:port,
separated by spaces
--population Required. Path to the .population file
containing descriptions of data sources and
species
--iter (Default: 3) Number of refinement sub-iterations
--first_iteration_fraction (Default: 1) Use this fraction of available
resolution for alignment in first sub-iteration,
increase linearly to 1.0 towards last
sub-iterations
--min_particles (Default: 1) Only use series with at least N
particles in the field of view
--cpu_memory Use CPU memory to store particle images during
refinement (GPU by default)
--weight_threshold (Default: 0.05) Refine each tilt/frame up to the
resolution at which the exposure weighting
function (B-factor) reaches this value
--refine_imagewarp Refine image warp with a grid of XxY dimensions.
Examples: leave blank = don't refine, '1x1',
'6x4'
--refine_particles Refine particle poses
--refine_mag Refine anisotropic magnification
--refine_doming Refine doming (frame series only)
--refine_stageangles Refine stage angles (tilt series only)
--refine_volumewarp Refine volume warp with a grid of XxYxZxT
dimensions (tilt series only). Examples: leave
blank = don't refine, '1x1x1x20', '4x6x1x41'
--refine_tiltmovies Refine tilt movie alignments (tilt series only)
--ctf_batch (Default: 32) Batch size for CTF refinements.
Lower = less memory, higher = faster
--ctf_minresolution (Default: 8) Use only species with at least this
resolution (in Angstrom) for CTF refinement
--ctf_defocus Refine defocus using a local search
--ctf_defocusexhaustive Refine defocus using a more exhaustive grid
search in the first sub-iteration; only works in
combination with ctf_defocus
--ctf_phase Refine phase shift (phase plate data only)
--ctf_cs Refine spherical aberration, which is also a
proxy for pixel size
--ctf_zernike3 Refine Zernike polynomials of 3rd order (beam
tilt, trefoil – fast)
--ctf_zernike5 Refine Zernike polynomials of 5th order (fast)
--ctf_zernike2 Refine Zernike polynomials of 2nd order (slow)
--ctf_zernike4 Refine Zernike polynomials of 4th order (slow)
--help Display this help screen.
--version Display version information.