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mparameters
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# Computer-specific setting
cluster_type none ! Set to "sge", "lsf", "slurm" or "pbs" when running on an SGE, LSF, SLURM or PBS cluster, otherwise set to "none".
nprocessor_ref 6 ! Number of CPUs to use during refinement.
nprocessor_rec 16 ! Number of CPUs to use during reconstruction.
mem_per_cpu 2048 ! Memory available per CPU (in MB).
# Refinement-specific parameters
MODE 1 ! 1, 2, 3 or 4. Refinement mode, normally 1. Set to 2 for additional search.
res_low_refinement 400.0 ! Low-resolution limit for particle alignment. Set to particle dimention or larger.
res_high_refinement 6.0 ! High-resolution limit for particle alignment.
res_high_class 6.0 ! High-resolution limit to calculate class membership (OCC).
thresh_reconst 0.8 ! Particles with scores below this value will not be included in the reconstruction.
nclasses 1 ! Number of classes to use.
# Search-specific parameters
res_search 30.0 ! High-resolution limit for orientational search.
thresh_refine 10.0 ! Score threshold above which search will not be performed.
DANG 200.0 ! Angular step for orientational search.
ITMAX 200 ! Number of repetitions of grid search with random starting angles.
Bsearch 2000.0 ! B-factor filtering (when > 0) applied during search.
# Dataset-specific parameters
data_input 14pf ! Root name for parameter and map files.
raw_images ../MTstack_selMT_DT
image_contrast P ! N or P. Set to N if particles are dark on bright background, otherwise set to P.
outer_radius 330.0 ! Outer radius of spehrical particle mask in Angstrom.
inner_radius 0.0 ! Inner radius of spehrical particle mask in Angstrom.
mol_mass 20000.0 ! Molecular mass in kDa of particle or helical segment. =1.32*400/80*14*110
Symmetry HP ! Symmetry of particle.
ALPHA -27.763 ! Helical twist angle in deg.
RISE 9.28 ! Helical rise in Angstrom.
NSUBUNITS 14 ! Number of unique subunits in one segment.
NSTARTS 1 ! Number of helocal starts.
STIFFNESS 0.0 ! Stregth of straightness restraint (small value = strong restraint).
pix_size 2.78 ! Pixel size of particle in Angstrom.
dstep 2.78 ! Pixel size of detector in micrometer.
Aberration 2.7 ! Sherical aberration coefficient in millimeter.
Voltage 300.0 ! Beam accelleration voltage in kilovolt.
Amp_contrast 0.1 ! Amplitude contrast.
# Expert parameters (for expert users)
XSTD -4 ! Tighter masking of 3D map (XSTD > 0) or particles (XSTD < 0).
PBC 10.0 ! Discriminate particles with different scores during reconstruction. Small values (5 - 10) discriminate more than large values (50 - 100).
refineangleinc 4 ! When larger than 1: Alternate between refinement of OCC and OCC + angles.
refineshiftinc 4 ! When larger than 1: Alternate between refinement of OCC and OCC + angles + shifts.
res_reconstruction 0.0 ! High-resolution limit of reconstruction. Normally set to Nyquist limit.
FMAG F ! T or F. Set to T to refine particle magnification. Not recommended in most cases.
FDEF F ! T or F. Set to T to refine defocus per micrograph. Not recommended in most cases.
FASTIG F ! T or F. Set to T to refine astigmatism. Not recommended in most cases.
FPART F ! T or F. Set to T to refine defocus for each particle. Not recommended in most cases.
FFILT T ! T or F. Set to T to apply optimal filter to reconstruction. Recommended in most cases.
FMATCH F ! T or F. Set to T to output matching projections. Only needed for diagnostics.
FBEAUT F ! T or F. Set to T to apply symmetry also in real space. Not needed in most cases.
FBOOST F ! T or F. Set to T to allow potential overfitting during refinement. Not recommended in most cases.
RBfactor 0.0 ! B-factor sharpening (when < 0) applied during refinement. Not recommended in most cases.
mp_cpus 16 ! Number of CPUs to use for each reconstruction job.
start_process 2
end_process 2
first_particle 1
last_particle 348514
increment 6971