Parameter Instance Visibility Review

This document inventories parameter visibility, not program visibility. Program visibility is intentionally excluded.

Each heading is one unique parameter key. Every row beneath it is a separate ui_program_input instance of that parameter in the named program. The value in Parameter visibility belongs only to that parameter instance and may differ between program contexts.

Edit Parameter visibility to standard, advanced, or developer. Required parameter instances must remain standard; optional instances may use any of the three values.

The initial parameter-instance assignments were inferred from the code:

1. Required parameter instances are standard.
2. Previously explicit parameter-instance visibility choices were preserved.
3. Otherwise-unclassified optional parameter instances in Developer programs were provisionally assigned developer.
4. Other otherwise-unclassified optional parameter instances were provisionally assigned advanced.

Inventory: 337 unique parameter keys and 1284 parameter instances. Parameter visibility totals: 455 Standard, 683 Advanced, and 146 Developer. 92 parameter keys currently have context-dependent visibility.

Parameter acf

Used by program	Parameter label	Required in this program	Parameter visibility
stackops	Autocorrelation, A * conjg(A)	no	advanced

Parameter algorithm

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	Algorithm for motion correction	no	advanced
preprocess	Algorithm for motion correction	no	advanced
tseries_motion_correct	Algorithm for motion correction	no	advanced

Parameter amsklp

Used by program	Parameter label	Required in this program	Parameter visibility
auto_spher_mask	Low-pass limit for envelope mask generation	yes	standard
automask	Low-pass limit for envelope mask generation	no	advanced
automask2D	Low-pass limit for envelope mask generation	no	advanced
refine3D	Low-pass limit for envelope mask generation	no	advanced
refine3D_auto	Low-pass limit for envelope mask generation	no	advanced

Parameter angastunit

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	Angle of astigmatism unit	no	advanced

Parameter angerr

Used by program	Parameter label	Required in this program	Parameter visibility
make_oris	Rotation angle error half-width	no	developer
oriops	Rotation angle error half-width	no	developer

Parameter angstep

Used by program	Parameter label	Required in this program	Parameter visibility
stackops	Angular stepsize	no	advanced

Parameter append

Used by program	Parameter label	Required in this program	Parameter visibility
selection	Append selection to existing	no	advanced

Parameter astigerr

Used by program	Parameter label	Required in this program	Parameter visibility
simulate_particles	Astigmatism error	no	advanced

Parameter astigthreshold

Used by program	Parameter label	Required in this program	Parameter visibility
pick_extract	Astigmatism rejection threshold	no	advanced

Parameter astigtol

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_estimate	Expected astigmatism	no	advanced
preprocess	Expected astigmatism	no	advanced

Parameter athres

Used by program	Parameter label	Required in this program	Parameter visibility
fsc_area_score	Cone half-angle	no	advanced
trajectory_make_projavgs	Angular threshold (degrees)	no	developer

Parameter automsk

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Perform envelope masking	no	standard
automask	Perform envelope masking	no	advanced
fsc_area_score	Perform envelope masking	no	advanced
nu_filt3D	Perform envelope masking	no	advanced
refine3D	Perform envelope masking	no	advanced
refine3D_multi	Perform envelope masking	no	advanced

Parameter autoscale

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Automatic down-scaling	no	advanced
refine3D_auto	Automatic down-scaling	no	advanced
refine3D_multi	Automatic down-scaling	no	advanced

Parameter avg

Used by program	Parameter label	Required in this program	Parameter visibility
stackops	Average stack	no	advanced

Parameter backgr_subtr

Used by program	Parameter label	Required in this program	Parameter visibility
extract	Perform micrograph background subtraction(new picker only)	no	advanced
pick	Perform micrograph background subtraction(new picker only)	no	advanced
reextract	Perform micrograph background subtraction(new picker only)	no	advanced

Parameter balance

Used by program	Parameter label	Required in this program	Parameter visibility
selection	Balanced selection of particles across classes	no	advanced

Parameter bandwidth_mode

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Diffusion-map bandwidth mode	no	advanced
denoise_project	Diffusion-map bandwidth mode	no	advanced
flex_analysis	Diffusion-map bandwidth mode	no	advanced
ppca_denoise	Diffusion-map bandwidth mode	no	advanced

Parameter bandwidth_tune

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Ferguson bandwidth multiplier (default 1)	no	advanced
denoise_project	Ferguson bandwidth multiplier (default 1)	no	advanced
flex_analysis	Ferguson bandwidth multiplier (default 1)	no	advanced
ppca_denoise	Ferguson bandwidth multiplier (default 1)	no	advanced

Parameter beamtilt

Used by program	Parameter label	Required in this program	Parameter visibility
assign_optics_groups	Use beamtilts in optics group assignment	no	developer
preproc	Use beamtilts in optics group assignment	no	developer

Parameter bfac

Used by program	Parameter label	Required in this program	Parameter visibility
ctfops	CTF B-factor	no	advanced
filter	B-factor of Gaussian low-/high-pass filter	no	advanced
motion_correct	B-factor applied to frames	no	advanced
postprocess	B-factor for sharpening	no	advanced
preprocess	B-factor applied to frames	no	advanced
simulate_movie	CTF B-factor	no	advanced
simulate_particles	CTF B-factor	no	advanced
tseries_make_pickavg	B-factor applied to frames	no	advanced
tseries_motion_correct	B-factor applied to frames	no	advanced
volops	B-factor for sharpening	no	advanced

Parameter bfacerr

Used by program	Parameter label	Required in this program	Parameter visibility
simulate_particles	B-factor error	no	advanced

Parameter binwidth

Used by program	Parameter label	Required in this program	Parameter visibility
automask	Envelope binary layers width	no	advanced

Parameter box

Used by program	Parameter label	Required in this program	Parameter visibility
crys_score	Particle box size	yes	standard
extract	Particle box size	no	standard
noisevol	Particle box size	yes	standard
print_dose_weights	Particle box size	yes	standard
print_fsc	Particle box size	no	advanced
print_magic_boxes	Particle box size	yes	standard
reextract	Particle box size	no	advanced
simulate_nanoparticle	Particle box size	yes	standard
simulate_noise	Particle box size	yes	standard

Parameter box_coarse

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Box size for coarse sieving	no	advanced

Parameter box_extract

Used by program	Parameter label	Required in this program	Parameter visibility
master	Force box size (px, optional)	no	developer
pick_extract	Extracted particle image size	no	advanced
tseries_extractor	Extracted particle image size	yes	standard

Parameter box_fine

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Box size for fine sieving	no	advanced

Parameter boxes

Used by program	Parameter label	Required in this program	Parameter visibility
print_project_field	output coordinates in JSON format	no	developer

Parameter boxfile

Used by program	Parameter label	Required in this program	Parameter visibility
track_particles	List of particle coordinates	yes	standard
tseries_motion_correct	List of particle coordinates	no	advanced

Parameter boxtab

Used by program	Parameter label	Required in this program	Parameter visibility
import_boxes	List of box files	yes	standard
import_movies	List of box files	no	advanced

Parameter cavg_ini

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	3D initialization on class averages	no	advanced

Parameter cavg_ini_ext

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	External class-average 3D initialization	no	advanced

Parameter cenlp

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Centering low-pass limit	no	advanced
abinitio2D_chunks	Centering low-pass limit	no	advanced
abinitio3D	Centering low-pass limit	no	advanced
abinitio3D_cavgs	Centering low-pass limit	no	advanced
abinitio3D_nano	Centering low-pass limit	no	advanced
autorefine3D_nano	Centering low-pass limit	no	advanced
center	Centering low-pass limit	no	developer
cluster2D_nano	Centering low-pass limit	no	advanced
refine3D	Centering low-pass limit	no	advanced
refine3D_nano	Centering low-pass limit	no	advanced
symaxis_search	Centering low-pass limit	no	advanced
symmetrize_map	Centering low-pass limit	no	advanced
symmetry_test	Centering low-pass limit	no	advanced
track_particles	Centering low-pass limit	no	advanced

Parameter center

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Center class averages	no	advanced
abinitio2D_chunks	Center class averages	no	advanced
abinitio3D	Center reference volume(s)	no	advanced
abinitio3D_cavgs	Center reference volume(s)	no	advanced
autorefine3D_nano	Center reference volume(s)	no	advanced
cluster2D_nano	Center class averages	no	advanced
mask	Center input volume	no	advanced
refine3D	Center reference volume(s)	no	advanced
refine3D_nano	Center reference volume(s)	no	advanced
symaxis_search	Center input volume	no	advanced
symmetrize_map	Center input volume	no	advanced
symmetry_test	Center input volume	no	advanced

Parameter center_pdb

Used by program	Parameter label	Required in this program	Parameter visibility
pdb2mrc	Whether to move the PDB atomic center to the center of the box	no	advanced

Parameter chunk_count_penalty

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Chunk-count penalty	no	developer

Parameter chunk_max_len

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Maximum latent chunk length	no	developer

Parameter chunk_max_shift

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Maximum boundary shift	no	developer

Parameter chunk_min_len

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Minimum latent chunk length	no	developer

Parameter chunk_mode

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Trajectory chunking mode	no	developer

Parameter ciffile

Used by program	Parameter label	Required in this program	Parameter visibility
cif2mrc	PDBx/mmCIF input coordinates file	yes	standard
cif2pdb	PDBx/mmCIF input coordinates file	yes	standard

Parameter class

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Optional class index to split	no	advanced
extract_subproj	2D class index	no	advanced
stackops	Class index	no	advanced

Parameter classtats

Used by program	Parameter label	Required in this program	Parameter visibility
oristats	Class statistics	no	developer

Parameter clip

Used by program	Parameter label	Required in this program	Parameter visibility
scale	Clipped box size	no	advanced
stack	Clipped box size	no	advanced

Parameter cls_init

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Scheme for initial class generation	no	advanced

Parameter clust_crit

Used by program	Parameter label	Required in this program	Parameter visibility
cluster_cavgs	Clustering criterion	no	advanced
cluster_cavgs_selection	Clustering criterion	no	advanced
cluster_stack	Clustering criterion	no	advanced
match_cavgs	Clustering criterion	no	developer
match_stacks	Clustering criterion	no	developer

Parameter clustind

Used by program	Parameter label	Required in this program	Parameter visibility
extract_subproj	Cluster index	no	advanced
select_clusters	Cluster index	no	developer

Parameter clustinds

Used by program	Parameter label	Required in this program	Parameter visibility
select_clusters	Comma separated cluster indices	no	developer

Parameter cn_stop

Used by program	Parameter label	Required in this program	Parameter visibility
symmetry_test	Rotational symmetry order stop index	no	advanced

Parameter combine_eo

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D	Whether e/o references are combined for final alignment(yes|no){no}	no	advanced
refine3D_auto	Whether e/o references are combined for final alignment(yes|no){no}	no	advanced

Parameter conical_fsc

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Conical FSC regularization	no	advanced
abinitio3D_cavgs	Conical FSC regularization	no	advanced
refine3D	Conical FSC regularization	no	advanced

Parameter continue

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D	Continue previous refinement	no	advanced
refine3D_auto	Continue previous refinement	no	advanced
refine3D_multi	Continue previous refinement	no	advanced
refine3D_nano	Continue previous refinement	no	advanced

Parameter cs

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Spherical aberration	yes	standard
import_movies	Spherical aberration	yes	standard
import_particles	Spherical aberration	yes	standard
master	Spherical aberration (mm)	yes	standard
mini_stream	Spherical aberration	yes	standard
preproc	Spherical aberration	yes	standard
simulate_movie	Spherical aberration	no	advanced
simulate_particles	Spherical aberration	no	advanced
tseries_import	Spherical aberration	yes	standard

Parameter ctf

Used by program	Parameter label	Required in this program	Parameter visibility
ctfops	CTF status	yes	standard
import_movies	CTF status	no	advanced
import_particles	CTF status	no	advanced
oriops	CTF status	no	developer
reimport_particles	CTF status	no	developer
simulate_particles	CTF status	yes	standard

Parameter ctf_correct_mode

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_correct	CTF correction mode	no	advanced

Parameter ctfpatch

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_estimate	Patch CTF estimation	no	advanced
preprocess	Patch CTF estimation	no	advanced

Parameter ctfresthreshold

Used by program	Parameter label	Required in this program	Parameter visibility
pick_extract	CTF Resolution rejection threshold	no	advanced
selection	CTF Resolution rejection threshold	no	advanced

Parameter ctfstats

Used by program	Parameter label	Required in this program	Parameter visibility
oristats	CTF statistics	no	developer

Parameter defocus

Used by program	Parameter label	Required in this program	Parameter visibility
simulate_movie	Underfocus	no	advanced
simulate_particles	Underfocus	no	advanced

Parameter deftab

Used by program	Parameter label	Required in this program	Parameter visibility
ctfops	CTF parameter file	no	advanced
import_movies	Pre-determined per-micrograph CTF parameters	no	advanced
import_particles	CTF parameter file	no	advanced
import_trajectory	CTF parameter file	no	advanced
simulate_particles	CTF parameter file	no	advanced

Parameter deselfile

Used by program	Parameter label	Required in this program	Parameter visibility
selection	File with deselection indices	no	advanced

Parameter dferr

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Underfocus error half-width	no	developer
simulate_particles	Underfocus error half-width	no	advanced

Parameter dfmax

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_estimate	Expected maximum defocus	no	advanced
preproc	Expected maximum defocus	no	developer
preprocess	Expected maximum defocus	no	advanced

Parameter dfmin

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_estimate	Expected minimum defocus	no	advanced
preproc	Expected minimum defocus	no	developer
preprocess	Expected minimum defocus	no	advanced
selection	Expected minimum defocus	no	advanced

Parameter dfunit

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	Underfocus unit	no	advanced

Parameter dir

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Project directory	no	advanced
pick	Output directory	no	advanced

Parameter dir_box

Used by program	Parameter label	Required in this program	Parameter visibility
extract	Box files directory	no	advanced

Parameter dir_exec

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D_stream	Previous run directory	no	developer
pick_extract	Previous run directory	no	advanced
sieve_cavgs	Previous run directory	no	advanced

Parameter dir_meta

Used by program	Parameter label	Required in this program	Parameter visibility
master	Input metadata directory	no	developer
preproc	Directory containing per-movie metadata in XML format	no	standard

Parameter dir_movies

Used by program	Parameter label	Required in this program	Parameter visibility
import_movies	Input movies directory	no	advanced
master	Input movies directory	yes	standard
preproc	Input movies directory	yes	standard

Parameter dir_preprocess

Used by program	Parameter label	Required in this program	Parameter visibility
master	Pre-existing preprocessing directory	no	developer

Parameter dir_prev

Used by program	Parameter label	Required in this program	Parameter visibility
preproc	Previous run directory	no	developer

Parameter dir_target

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D_stream	Target directory	yes	standard
assign_optics	Target directory	yes	standard
gen_pickrefs	Target directory	yes	standard
pick_extract	Target directory	yes	standard
sieve_cavgs	Target directory	yes	standard

Parameter dm_alpha

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Diffusion-map density normalization (default 0)	no	advanced
denoise_project	Diffusion-map density normalization (default 0)	no	advanced
ppca_denoise	Diffusion-map density normalization (default 0)	no	advanced

Parameter e1

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Rotation along Phi	no	developer
volops	Rotation along Phi	no	advanced

Parameter e2

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Rotation along Theta	no	developer
volops	Rotation along Theta	no	advanced

Parameter e3

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Rotation along Psi	no	developer
volops	Rotation along Psi	no	advanced

Parameter edge

Used by program	Parameter label	Required in this program	Parameter visibility
automask	Envelope mask soft edge	no	advanced
automask2D	Envelope mask soft edge	no	advanced
mask	Envelope mask soft edge	no	advanced

Parameter eer_fraction

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	# of EER frames to fraction together	no	advanced
preproc	# of EER frames to fraction together	no	developer
preprocess	# of EER frames to fraction together	no	advanced

Parameter element

Used by program	Parameter label	Required in this program	Parameter visibility
analysis2D_nano	Atom element name: Au, Pt etc.	yes	standard
atoms_rmsd	Atom element name: Au, Pt etc.	yes	standard
atoms_stats	Atom element name: Au, Pt etc.	yes	standard
autorefine3D_nano	Atom element name: Au, Pt etc.	yes	standard
conv_atom_denoise	Atom element name: Au, Pt etc.	yes	standard
core_atoms_analysis	Atom element name: Au, Pt etc.	yes	standard
crys_score	Atom element name: Au, Pt etc.	yes	standard
detect_atoms	Atom element name: Au, Pt etc.	yes	standard
simulate_nanoparticle	Atom element name: Au, Pt etc.	no	advanced

Parameter envfsc

Used by program	Parameter label	Required in this program	Parameter visibility
reconstruct3D	Envelope mask e/o maps for FSC	no	advanced
refine3D	Envelope mask e/o maps for FSC	no	advanced

Parameter even

Used by program	Parameter label	Required in this program	Parameter visibility
make_oris	Generate even projections	no	developer
simulate_particles	Generate even projections	no	advanced

Parameter fbody

Used by program	Parameter label	Required in this program	Parameter visibility
fsc_area_score	Output file body	no	advanced
motion_correct	Template output micrograph name	no	advanced
preprocess	Template output micrograph name	no	advanced
track_particles	Template output tracked series	yes	standard

Parameter filetab

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	List of files	yes	standard
import_movies	List of movie files	no	advanced
mini_stream	List of files	yes	standard
model_cavgs_rejection	Analysis file table	no	advanced
scale	Stacks list	no	advanced
stack	Stacks list	yes	standard
tsegmaps_core_finder	Volumes list	yes	standard
tseries_import	List of individual movie frame files	yes	standard
volanalyze	Volumes list	yes	standard
volcluster	Volumes list	yes	standard

Parameter fill_holes

Used by program	Parameter label	Required in this program	Parameter visibility
binarize	Fill holes	no	developer

Parameter filt_mode

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Filtering mode	no	advanced
refine3D_auto	Filtering mode	no	advanced
refine3D_multi	Filtering mode	no	advanced

Parameter filter

Used by program	Parameter label	Required in this program	Parameter visibility
filter	Filter type(bs|nlmean|no){no}	no	advanced
track_particles	Alternative filter for particle tracking	no	advanced

Parameter fit_phshift

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Fit CTF phase shift	no	developer
ctf_estimate	Fit CTF phase shift	no	advanced
master	Phase plate	no	developer
mini_stream	Fit CTF phase shift	no	advanced
preproc	Fit CTF phase shift	no	standard
preprocess	Fit CTF phase shift	no	advanced

Parameter flipgain

Used by program	Parameter label	Required in this program	Parameter visibility
fractionate_movies	Flip the gain reference	no	advanced
master	Gain processing	no	developer
motion_correct	Flip the gain reference	no	advanced
preproc	Flip the gain reference	no	developer
preprocess	Flip the gain reference	no	advanced

Parameter fname

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_register	PDB file list	yes	standard
crys_score	PDB file list	yes	standard
info_image	Name of image file	yes	standard
model_cavgs_rejection	Quality model output	no	advanced
write_mic_filetab	Filename micrograph list	yes	standard

Parameter force_lp_range

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Force low-pass range	no	advanced

Parameter frac_best

Used by program	Parameter label	Required in this program	Parameter visibility
bootstrap_cavgs	Anchor fraction	no	developer
sample_classes	Fraction of best particles to sample from	no	advanced

Parameter frac_diam

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_rmsd	Fraction of atomic diameter	no	advanced
core_atoms_analysis	Fraction of atomic diameter	no	developer

Parameter frac_worst

Used by program	Parameter label	Required in this program	Parameter visibility
sample_classes	Fraction of worst particles to sample from	no	advanced

Parameter fraca

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Amplitude contrast fraction	no	developer
import_movies	Amplitude contrast fraction	yes	standard
import_particles	Amplitude contrast fraction	yes	standard
master	Amplitude contrast fraction	yes	standard
mini_stream	Amplitude contrast fraction	no	advanced
preproc	Amplitude contrast fraction	yes	standard
simulate_movie	Amplitude contrast fraction	no	advanced
simulate_particles	Amplitude contrast fraction	no	advanced
tseries_import	Amplitude contrast fraction	yes	standard

Parameter fraction_dose_target

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	EER fraction dose target (e/Ang^2)	no	advanced
preproc	EER fraction dose target (e/Ang^2)	no	standard
preprocess	EER fraction dose target (e/Ang^2)	no	advanced

Parameter frcs

Used by program	Parameter label	Required in this program	Parameter visibility
filter	Projection FRCs file	no	advanced
print_fsc	Projection FRCs file	no	advanced

Parameter fromf

Used by program	Parameter label	Required in this program	Parameter visibility
fractionate_movies	Starting frame	no	advanced
track_particles	Frame to start tracking from	no	advanced
tseries_make_pickavg	Frame to start averaging from	no	advanced

Parameter fromp

Used by program	Parameter label	Required in this program	Parameter visibility
extract_subproj	From index	no	advanced
extract_substk	From index	no	advanced
scale	First stack index	no	advanced
stackops	From particle index	no	advanced
trajectory_reconstruct3D	From particle index	no	developer

Parameter fsc

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_correct	FSC file	no	advanced
filter	FSC file	no	advanced
postprocess	FSC file	no	advanced
print_fsc	FSC file	no	advanced

Parameter gainref

Used by program	Parameter label	Required in this program	Parameter visibility
master	Gain reference	no	developer
motion_correct	Gain reference	no	standard
preproc	Gain reference	no	standard
preprocess	Gain reference	no	advanced

Parameter graph

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Class split graph	no	advanced
denoise_project	Diffusion graph	no	advanced

Parameter greedy_sampling

Used by program	Parameter label	Required in this program	Parameter visibility
sample_classes	Greedy balanced selection	no	advanced
selection	Greedy balanced selection	no	advanced

Parameter guinier

Used by program	Parameter label	Required in this program	Parameter visibility
volops	Guinier plot	no	advanced

Parameter hp

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	High-pass limit	no	advanced
abinitio2D_chunks	High-pass limit	no	advanced
abinitio3D	High-pass limit	no	advanced
abinitio3D_cavgs	High-pass limit	no	advanced
abinitio3D_nano	High-pass limit	no	advanced
autorefine3D_nano	High-pass limit	no	advanced
cluster2D_nano	High-pass limit	no	advanced
cluster_cavgs	High-pass limit	no	advanced
cluster_cavgs_selection	High-pass limit	no	advanced
cluster_stack	High-pass limit	no	advanced
ctf_estimate	High-pass limit	no	advanced
dock_volpair	High-pass limit	no	advanced
filter	High-pass limit	no	advanced
fsc	High-pass limit	no	advanced
match_cavgs	High-pass limit	no	developer
match_stacks	High-pass limit	yes	standard
ppca_denoise	High-pass limit	no	advanced
refine3D	High-pass limit	no	advanced
refine3D_nano	High-pass limit	no	advanced
symaxis_search	High-pass limit	no	advanced
symmetrize_map	High-pass limit	no	advanced
symmetry_test	High-pass limit	no	advanced
track_particles	High-pass limit	no	advanced
trajectory_denoise	High-pass limit	no	advanced
volanalyze	High-pass limit	yes	standard
volcluster	High-pass limit	no	advanced
volops	High-pass limit	no	advanced

Parameter hp_ctf_estimate

Used by program	Parameter label	Required in this program	Parameter visibility
preprocess	High-pass limit for CTF parameter estimation	no	advanced

Parameter icefracthreshold

Used by program	Parameter label	Required in this program	Parameter visibility
pick_extract	Ice Fraction rejection threshold	no	advanced
selection	Ice Fraction rejection threshold	no	advanced

Parameter icm

Used by program	Parameter label	Required in this program	Parameter visibility
autorefine3D_nano	Whether to perform ICM filtering of reference(s)	no	advanced
flex_analysis	Automatic diffusion-mode selection	no	advanced
refine3D_nano	Whether to perform ICM filtering of reference(s)	no	advanced
uniform_filter3D	Whether to perform ICM filtering of reference(s)	no	advanced

Parameter imgkind

Used by program	Parameter label	Required in this program	Parameter visibility
postprocess	Volume kind	no	advanced

Parameter import_dir

Used by program	Parameter label	Required in this program	Parameter visibility
import_starproject	Import directory	yes	standard

Parameter import_type

Used by program	Parameter label	Required in this program	Parameter visibility
import_starproject	Import type	no	standard

Parameter infile

Used by program	Parameter label	Required in this program	Parameter visibility
model_cavgs_rejection	Quality model input	no	advanced
selection	File with selection state (0/1) flags	no	advanced
tseries_extractor	Selected particle trajectory	yes	standard

Parameter job_memory_per_task

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Memory per computing node	no	advanced
update_project	Memory per computing node	no	advanced

Parameter json

Used by program	Parameter label	Required in this program	Parameter visibility
print_project_field	output in JSON format	no	developer

Parameter k_nn

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Diffusion graph neighbors (default 10; try 5-30)	no	advanced
denoise_project	Diffusion graph neighbors (default 10; try 5-30)	no	advanced
flex_analysis	Nearest neighbors (default 100)	no	advanced
ppca_denoise	Diffusion graph neighbors (default 5; try 5-30)	no	advanced
trajectory_denoise	Diffusion graph neighbors (default 5; try 5-30)	no	advanced

Parameter kpca_backend

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise	Kernel PCA backend	no	advanced
ppca_denoise_classes	Kernel PCA backend	no	advanced
trajectory_denoise	Kernel PCA backend	no	advanced

Parameter kpca_ker

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise	Kernel PCA kernel	no	advanced
ppca_denoise_classes	Kernel PCA kernel	no	advanced
trajectory_denoise	Kernel PCA kernel	no	advanced

Parameter kpca_nystrom_local_nbrs

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise	Nyström max local support neighbors (default 96; try 96, 128)	no	advanced
ppca_denoise_classes	Nyström max local support neighbors (default 96; try 96, 128)	no	advanced
trajectory_denoise	Nyström max local support neighbors (default 96; try 96, 128)	no	advanced

Parameter kpca_nystrom_npts

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise	Nyström landmark count (0 => auto=max(128,2*neigs), capped at 512; try 256, 512)	no	advanced
ppca_denoise_classes	Nyström landmark count (0 => auto=max(128,2*neigs), capped at 512; try 256, 512)	no	advanced
trajectory_denoise	Nyström landmark count (0 => auto=max(128,2*neigs), capped at 512; try 256, 512)	no	advanced

Parameter kpca_rbf_gamma

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise	RBF gamma (0 => auto)	no	advanced
ppca_denoise_classes	RBF gamma (0 => auto)	no	advanced
trajectory_denoise	RBF gamma (0 => auto)	no	advanced

Parameter kv

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Acceleration voltage	yes	standard
import_movies	Acceleration voltage	yes	standard
import_particles	Acceleration voltage	yes	standard
master	Acceleration voltage (kV)	yes	standard
mini_stream	Acceleration voltage	yes	standard
preproc	Acceleration voltage	yes	standard
print_dose_weights	Acceleration voltage	no	advanced
simulate_movie	Acceleration voltage	no	advanced
simulate_particles	Acceleration voltage	no	advanced
tseries_import	Acceleration voltage	yes	standard

Parameter lambda

Used by program	Parameter label	Required in this program	Parameter visibility
filter	BS smoother lambda	no	advanced
icm2D	ICM lambda regularization parameter	no	advanced
icm3D	ICM lambda regularization parameter	no	advanced
uniform_filter3D	ICM lambda regularization parameter	no	advanced

Parameter lp

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Low-pass limit	no	advanced
abinitio2D_chunks	Low-pass limit	no	advanced
abinitio3D	Low-pass limit	no	advanced
autorefine3D_nano	Initial low-pass limit	yes	standard
cluster2D_nano	Static low-pass limit	no	advanced
cluster_cavgs	Low-pass limit	no	advanced
cluster_cavgs_selection	Low-pass limit	no	advanced
cluster_stack	Low-pass limit	yes	standard
ctf_estimate	Low-pass limit	no	advanced
dock_volpair	Low-pass limit	no	advanced
estimate_diam	low-pass limit in Angstroms{7.}	no	advanced
filter	Low-pass limit	no	advanced
flex_analysis	Low-pass limit	no	standard
fsc	Low-pass limit	no	advanced
match_cavgs	Low-pass limit	no	developer
match_stacks	Low-pass limit	yes	standard
pick	Low-pass limit	no	advanced
postprocess	Low-pass limit for map filtering	no	advanced
ppca_denoise	Low-pass limit	no	advanced
refine3D	Static low-pass limit	no	advanced
refine3D_nano	Static low-pass limit	no	advanced
symaxis_search	Low-pass limit	no	advanced
symmetrize_map	Low-pass limit	no	advanced
symmetry_test	Low-pass limit	no	advanced
trajectory_denoise	Low-pass limit	no	advanced
trajectory_reconstruct3D	Low-pass limit	no	developer
volanalyze	Low-pass limit	yes	standard
volcluster	Low-pass limit	yes	standard
volops	Low-pass limit	no	advanced

Parameter lp_backgr

Used by program	Parameter label	Required in this program	Parameter visibility
mask	Background low-pass resolution	no	advanced
refine3D	Background low-pass resolution	no	advanced

Parameter lp_ctf_estimate

Used by program	Parameter label	Required in this program	Parameter visibility
preprocess	Low-pass limit for CTF parameter estimation	no	advanced

Parameter lp_pick

Used by program	Parameter label	Required in this program	Parameter visibility
pick_extract	Low-pass limit for picking	no	advanced
track_particles	Low-pass limit in Angs	no	advanced

Parameter lplim_crit

Used by program	Parameter label	Required in this program	Parameter visibility
fsc_area_score	Low-pass limit FSC criterion	no	advanced
refine3D	Low-pass limit FSC criterion	no	advanced

Parameter lpstart

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Initial low-pass limit	no	advanced
abinitio3D	Starting low-pass limit	no	advanced
abinitio3D_cavgs	Starting low-pass limit	no	advanced
abinitio3D_nano	Starting low-pass limit	no	advanced
cluster2D_nano	Initial low-pass limit	no	advanced
motion_correct	Initial low-pass limit	no	advanced
particle_sieving	Initial low-pass limit	no	advanced
preprocess	Initial low-pass limit for movie alignment	no	advanced
tseries_make_pickavg	Initial low-pass limit	no	advanced
tseries_motion_correct	Initial low-pass limit	no	advanced
uniform_filter2D	Starting resolution limit	yes	standard
uniform_filter3D	Starting resolution limit	yes	standard

Parameter lpstart_ini3D

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Starting low-pass limit ini3D	no	advanced

Parameter lpstop

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Final low-pass limit	no	advanced
abinitio2D_chunks	Final low-pass limit	no	advanced
abinitio3D	Final low-pass limit	no	advanced
abinitio3D_cavgs	Final low-pass limit	no	advanced
abinitio3D_nano	Final low-pass limit	no	advanced
cluster2D_nano	Final low-pass limit	no	advanced
motion_correct	Final low-pass limit	no	advanced
preprocess	Final low-pass limit for movie alignment	no	advanced
refine3D	Low-pass limit for frequency limited refinement	no	advanced
refine3D_multi	Low-pass limit for frequency limited refinement	no	advanced
tseries_make_pickavg	Final low-pass limit	no	advanced
tseries_motion_correct	Final low-pass limit	no	advanced
uniform_filter2D	Stopping resolution limit	yes	standard
uniform_filter3D	Stopping resolution limit	yes	standard

Parameter lpstop_coarse

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Final low-pass limit for coarse sieving	no	advanced

Parameter lpstop_fine

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Final low-pass limit for fine sieving	no	advanced

Parameter lpstop_ini3D

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Final low-pass limit ini3D	no	advanced

Parameter makemovie

Used by program	Parameter label	Required in this program	Parameter visibility
stackops	Whether to make a movie	no	advanced

Parameter max_dose

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	Maximum dose threshold(e/A2)	no	advanced
preproc	Maximum dose threshold(e/A2)	no	developer
preprocess	Maximum dose threshold(e/A2)	no	advanced

Parameter maxits

Used by program	Parameter label	Required in this program	Parameter visibility
autorefine3D_nano	Max iterations	no	advanced
cluster2D_nano	Max iterations	no	advanced
reconstruct3D_pcg	Max iterations	no	developer
refine3D	Max iterations	no	advanced
refine3D_auto	Max iterations	no	advanced
refine3D_multi	Max iterations	no	advanced
refine3D_nano	Max iterations	no	advanced
trajectory_reconstruct3D	Max iterations	no	developer

Parameter maxnchunks

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Max # of chunks to process	no	advanced

Parameter maxpop

Used by program	Parameter label	Required in this program	Parameter visibility
assign_optics_groups	Maximum number of movies/micrographs/stacks in each optics group	no	developer

Parameter mcconvention

Used by program	Parameter label	Required in this program	Parameter visibility
fractionate_movies	Movie alignment convention	no	advanced
motion_correct	Frame of reference during movie alignment	no	advanced
preprocess	Frame of reference during movie alignment	no	advanced

Parameter mcpatch

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	Patch-based motion correction	no	advanced
preprocess	Patch-based motion correction	no	advanced
tseries_make_pickavg	Patch-based motion correction	no	advanced
tseries_motion_correct	Patch-based motion correction	no	advanced

Parameter mcpatch_thres

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	Use motion correction patch threshold	no	advanced
preprocess	Use motion correction patch threshold	no	advanced

Parameter mirr

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Mirror orientations	no	developer
postprocess	Perform mirroring	no	advanced
stackops	Perform mirroring	no	advanced
volops	Perform mirroring	no	advanced

Parameter ml_reg

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D	ML regularization	no	advanced
refine3D_multi	ML regularization	no	advanced

Parameter moldiam

Used by program	Parameter label	Required in this program	Parameter visibility
cluster2D_nano	Molecular diameter	no	advanced
pick	Molecular diameter	no	advanced
pick_extract	Molecular diameter	no	advanced
print_magic_boxes	Molecular diameter	no	developer
simulate_nanoparticle	Molecular diameter	no	advanced

Parameter moldiam_max

Used by program	Parameter label	Required in this program	Parameter visibility
mini_stream	Max molecular diameter	no	advanced
pick	Max molecular diameter	no	advanced
pick_extract	Max molecular diameter	no	advanced

Parameter mskdiam

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Mask diameter	yes	standard
abinitio2D_chunks	Mask diameter	yes	standard
abinitio2D_stream	Mask diameter	no	standard
abinitio3D	Mask diameter	yes	standard
abinitio3D_cavgs	Mask diameter	yes	standard
abinitio3D_nano	Mask diameter	yes	standard
automask2D	Mask diameter	yes	standard
autorefine3D_nano	Mask diameter	yes	standard
bootstrap_rec3D	Mask diameter	yes	standard
cavgseoproc_nano	Mask diameter	yes	standard
cavgsproc_nano	Mask diameter	yes	standard
cls_split	Mask diameter	no	standard
cluster2D_nano	Mask diameter	yes	standard
cluster_cavgs	Mask diameter	yes	standard
cluster_cavgs_selection	Mask diameter	yes	standard
cluster_stack	Mask diameter	yes	standard
conv_atom_denoise	Mask diameter	yes	standard
denoise_project	Mask diameter	no	standard
detect_atoms	Mask diameter	no	advanced
dock_volpair	Mask diameter	yes	standard
estimate_diam	Mask diameter	yes	standard
flex_analysis	Mask diameter	no	standard
fsc	Mask diameter	yes	standard
fsc_area_score	Mask diameter	yes	standard
mask	Mask diameter	no	advanced
match_cavgs	Mask diameter	yes	standard
match_stacks	Mask diameter	yes	standard
model_cavgs_rejection	Mask diameter	yes	standard
normalize	Mask diameter	yes	standard
nu_filt3D	Mask diameter	yes	standard
postprocess	Mask diameter	yes	standard
ppca_denoise	Mask diameter	no	advanced
ppca_volvar	Mask diameter	no	developer
ptclsproc_nano	Mask diameter	yes	standard
reconstruct3D	Mask diameter	yes	standard
reconstruct3D_pcg	Mask diameter	no	developer
refine3D	Mask diameter	yes	standard
refine3D_auto	Mask diameter	yes	standard
refine3D_multi	Mask diameter	yes	standard
refine3D_nano	Mask diameter	yes	standard
reproject	Mask diameter	no	advanced
sieve_cavgs	Mask diameter	no	standard
simulate_particles	Mask diameter	yes	standard
symaxis_search	Mask diameter	yes	standard
symmetrize_map	Mask diameter	yes	standard
symmetry_test	Mask diameter	yes	standard
trajectory_denoise	Mask diameter	no	advanced
trajectory_make_projavgs	Mask diameter	yes	standard
trajectory_reconstruct3D	Mask diameter	yes	standard
uniform_filter2D	Mask diameter	yes	standard
uniform_filter3D	Mask diameter	yes	standard
validate_cavgs_vs_model	Mask diameter	yes	standard
volanalyze	Mask diameter	yes	standard
volcluster	Mask diameter	yes	standard
volops	Mask diameter	no	advanced

Parameter mskdiam_detect

Used by program	Parameter label	Required in this program	Parameter visibility
autorefine3D_nano	Detect-atoms mask diameter	no	advanced

Parameter mul

Used by program	Parameter label	Required in this program	Parameter visibility
make_cavgs	Shift multiplication factor	no	advanced
oriops	Shift multiplication factor	no	developer
volops	Multiplication factor	no	advanced

Parameter multi_moldiams

Used by program	Parameter label	Required in this program	Parameter visibility
pick	Comma-separated molecular diameters with which to execute multiple gaussian pick	no	advanced

Parameter multivol_mode

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Multi-volume ab initio mode	no	advanced
abinitio3D_cavgs	Multi-volume class-average ab initio mode	no	advanced
refine3D_multi	Multi-volume refinement mode	no	advanced

Parameter nang_nbrs

Used by program	Parameter label	Required in this program	Parameter visibility
flex_analysis	Angular candidate cap (default 1000)	no	advanced

Parameter nboxes_max

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Max # boxes per micrograph	no	developer
pick	Max # boxes per micrograph	no	advanced

Parameter nchunks

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D_chunks	Number of chunks	no	advanced
sieve_cavgs	Number of subsets to classify simultaneously	yes	standard
trajectory_reconstruct3D	Number of temporal chunks	no	developer

Parameter nchunks_max

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Maximum automatic chunk count	no	developer

Parameter nchunks_min

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Minimum automatic chunk count	no	developer

Parameter nchunksperset

Used by program	Parameter label	Required in this program	Parameter visibility
sieve_cavgs	Number of subsets to group	no	standard

Parameter ncls

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Number of 2D clusters	yes	standard
abinitio2D_stream	Maximum number of 2D clusters	yes	standard
center2D_nano	Number of 2D clusters	yes	standard
cls_split	Fixed number of subclasses (0 => auto)	no	advanced
cluster_cavgs	Number of clusters	no	advanced
cluster_stack	Number of clusters	no	advanced
make_cavgs	Number of 2D clusters	no	advanced
make_oris	Number of random class labels	no	developer
pick	Cluster input pickrefs before template generation	no	advanced
sieve_cavgs	Number of 2D clusters	yes	standard
volcluster	Number of 2D clusters	no	advanced

Parameter ncls_coarse

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Number of clusters for coarse sieving	no	advanced

Parameter ncls_fine

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Number of clusters for fine sieving	no	advanced

Parameter ncunits

Used by program	Parameter label	Required in this program	Parameter visibility
track_particles	Concurrent particle trackers	yes	standard

Parameter ndev

Used by program	Parameter label	Required in this program	Parameter visibility
binarize	Binarization threshold	no	developer
pick	# of sigmas for outlier detection	no	standard

Parameter ndiscrete

Used by program	Parameter label	Required in this program	Parameter visibility
make_oris	Number of discrete projection directions	no	developer
oriops	Number of discrete projection directions	no	developer

Parameter neg

Used by program	Parameter label	Required in this program	Parameter visibility
ctfops	Invert contrast	no	advanced
reproject	Invert contrast	no	advanced
stackops	Invert contrast	no	advanced
track_particles	Invert contrast	no	advanced
volops	Invert contrast	no	advanced

Parameter neigs

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Number of eigencomponents (0 => auto scan; default 200)	no	advanced
denoise_project	Number of eigencomponents (0 => auto scan; default 200)	no	advanced
flex_analysis	Maximum number of diffusion modes (default 15)	no	advanced
ppca_denoise	Number of eigencomponents (0 => auto for Nyström kPCA; default 160; try 128, 160)	yes	standard
ppca_denoise_classes	# eigenvecs (0 => auto for Nyström kPCA; default 160; try 128, 160)	no	advanced
ppca_volvar	# eigenvecs	yes	standard
trajectory_denoise	Number of diffusion-map components (0 => auto; default 0)	no	advanced
trajectory_reconstruct3D	Flex latent dimensions	no	developer

Parameter newbox

Used by program	Parameter label	Required in this program	Parameter visibility
scale	Scaled box size	no	advanced

Parameter nframes

Used by program	Parameter label	Required in this program	Parameter visibility
print_dose_weights	Number of frames	yes	standard
simulate_movie	Number of frames	no	advanced
simulate_particles	# of particle frames	no	advanced

Parameter nframesgrp

Used by program	Parameter label	Required in this program	Parameter visibility
stackops	Number of stack entries to group & average	no	advanced
track_particles	Number of contigous frames to average	no	advanced
tseries_make_pickavg	# contigous frames to average	no	advanced
tseries_motion_correct	# frames in time moving time window	no	advanced

Parameter ngrow

Used by program	Parameter label	Required in this program	Parameter visibility
automask2D	# layers to grow	no	advanced

Parameter nicedispid

Used by program	Parameter label	Required in this program	Parameter visibility
master	Optics group offset delta multiplier	no	developer

Parameter ninipick

Used by program	Parameter label	Required in this program	Parameter visibility
preproc	Number of micrographs to perform initial picking preprocessing on	no	developer

Parameter nmics

Used by program	Parameter label	Required in this program	Parameter visibility
gen_pickrefs	Number of micrographs to import	no	advanced
particle_sieving	Max # of micrographs per chunk	no	advanced

Parameter nmoldiams

Used by program	Parameter label	Required in this program	Parameter visibility
pick	Number of molecular diameters to investigate	no	advanced
pick_extract	Number of molecular diameters to investigate	no	advanced

Parameter noise_norm

Used by program	Parameter label	Required in this program	Parameter visibility
normalize	Noise normalize	no	advanced

Parameter norm

Used by program	Parameter label	Required in this program	Parameter visibility
normalize	Normalize	no	advanced

Parameter nparts

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Number of computing nodes	no	standard
abinitio2D_chunks	Number of computing nodes	no	standard
abinitio2D_stream	Number of computing nodes	yes	standard
abinitio3D	Number of computing nodes	no	standard
abinitio3D_cavgs	Number of computing nodes	no	standard
abinitio3D_nano	Number of computing nodes	no	advanced
bootstrap_cavgs	Number of computing nodes	no	developer
bootstrap_rec3D	Number of computing nodes	no	developer
cls_split	Number of computing nodes	no	standard
cluster2D_nano	Number of computing nodes	no	advanced
ctf_estimate	Number of computing nodes	yes	standard
denoise_project	Number of computing nodes	no	standard
extract	Number of computing nodes	yes	standard
flex_analysis	Number of computing nodes	no	standard
fractionate_movies	Number of computing nodes	yes	standard
gen_pspecs_and_thumbs	Number of computing nodes	yes	standard
make_cavgs	Number of computing nodes	yes	standard
motion_correct	Number of computing nodes	yes	standard
particle_sieving	Number of chunks classified simultaneously	no	standard
pick	Number of computing nodes	yes	standard
pick_extract	Number of computing nodes	yes	standard
preproc	Number of computing nodes	yes	standard
preprocess	Number of computing nodes	yes	standard
prune_project	Number of computing nodes	yes	standard
reconstruct3D	Number of computing nodes	no	advanced
reextract	Number of computing nodes	yes	standard
refine3D	Number of computing nodes	no	standard
refine3D_auto	Number of computing nodes	yes	standard
refine3D_multi	Number of computing nodes	yes	standard
refine3D_nano	Number of computing nodes	no	advanced
sample_classes	Number of partitions in balancing	no	advanced
selection	Number of partitions in balancing	no	advanced
sieve_cavgs	Number of computing nodes	yes	standard
split	Number of computing nodes	yes	standard
split_stack	Number of parts balanced splitting of the stack	yes	standard
trajectory_reconstruct3D	Number of computing nodes	no	developer
tseries_motion_correct	Number of computing nodes	yes	standard

Parameter npreimages

Used by program	Parameter label	Required in this program	Parameter visibility
flex_analysis	Representative state volumes (default 8)	no	advanced

Parameter nptcls

Used by program	Parameter label	Required in this program	Parameter visibility
make_oris	Number of per-particle orientations	yes	standard
simulate_noise	Number of particles	yes	standard
simulate_particles	Number of particles	yes	standard

Parameter nptcls_coarse

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Target # of particles per coarse chunk	no	advanced

Parameter nptcls_fine

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Target # of particles per fine chunk	no	advanced

Parameter nptcls_per_cls

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D_chunks	Number of particles per cluster	no	standard
analysis2D_nano	Number of particles per cluster	no	advanced
check_refpick	Number of particles per class	no	developer
cluster2D_nano	Number of particles per cluster	no	advanced
mini_stream	Number of particles per class	no	advanced
sieve_cavgs	Number of particles per cluster	yes	standard

Parameter nptcls_per_part

Used by program	Parameter label	Required in this program	Parameter visibility
sample_classes	Number of ptcls per part to select when balancing	no	advanced
selection	Number of ptcls per part to select when balancing	no	advanced

Parameter nran

Used by program	Parameter label	Required in this program	Parameter visibility
selection	Number of random samples	no	advanced
stackops	Number of random samples	no	advanced

Parameter nrestarts

Used by program	Parameter label	Required in this program	Parameter visibility
autorefine3D_nano	Number of restarts	no	advanced

Parameter nsample

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Number of particles to sample	no	advanced
abinitio3D	Number of particles to sample	no	standard
abinitio3D_nano	Number of particles to sample	no	advanced
sample_classes	Number of particles to sample	no	advanced

Parameter nsample_coarse

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Number of particles to sample in coarse sieving	no	advanced

Parameter nsample_fine

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Number of particles to sample in fine sieving	no	advanced

Parameter nspace

Used by program	Parameter label	Required in this program	Parameter visibility
autorefine3D_nano	Number of projection directions	no	advanced
denoise_project	Number of projection directions	no	advanced
flex_analysis	Number of projection directions	yes	standard
fsc_area_score	Number of cone axes	no	advanced
make_cavgs	Number of projection directions	no	advanced
oristats	Number of projection directions	no	developer
refine3D	Number of projection directions	no	advanced
refine3D_nano	Number of projection directions	no	advanced
reproject	Number of projection directions	yes	standard
trajectory_make_projavgs	Number of projection directions	no	developer
vizoris	Number of projection directions	no	advanced

Parameter nspace_sub

Used by program	Parameter label	Required in this program	Parameter visibility
denoise_project	SO3 mixture subspace size	no	advanced

Parameter nstages

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Last ab initio stage to run	no	advanced
estimate_lpstages	Number of low-pass limit stages	yes	standard

Parameter nstates

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Number of states	no	standard
abinitio3D_cavgs	Number of states	no	standard
bootstrap_rec3D	Number of states	no	developer
make_oris	Number of random state labels	no	developer
noisevol	Number states	no	advanced
oriops	Number of random state labels	no	developer
ptcl3D_state_consensus	Number of states	no	advanced
refine3D	Number of states	no	advanced
refine3D_multi	Number of states	no	advanced

Parameter nsubcls_max

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Maximum subclass trial count in auto mode (default 10)	no	advanced

Parameter nsubcls_min

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Minimum subclass trial count in auto mode (default 3)	no	advanced

Parameter nthr

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Number of threads per computing node, give 0 if unsure	yes	standard
abinitio2D_chunks	Number of threads per computing node, give 0 if unsure	yes	standard
abinitio2D_stream	Number of threads per computing node, give 0 if unsure	yes	standard
abinitio3D	Number of threads per computing node, give 0 if unsure	yes	standard
abinitio3D_cavgs	Number of threads per computing node, give 0 if unsure	yes	standard
abinitio3D_nano	Number of threads per computing node, give 0 if unsure	yes	standard
analysis2D_nano	Number of threads per computing node, give 0 if unsure	yes	standard
assign_optics	Number of threads per computing node, give 0 if unsure	yes	standard
atoms_register	Number of threads per computing node, give 0 if unsure	yes	standard
atoms_stats	Number of threads per computing node, give 0 if unsure	yes	standard
auto_spher_mask	Number of threads per computing node, give 0 if unsure	yes	standard
automask	Number of threads per computing node, give 0 if unsure	yes	standard
automask2D	Number of threads per computing node, give 0 if unsure	yes	standard
autorefine3D_nano	Number of threads per computing node, give 0 if unsure	yes	standard
binarize	Number of threads per computing node, give 0 if unsure	yes	standard
bootstrap_cavgs	Number of threads per computing node, give 0 if unsure	yes	standard
bootstrap_rec3D	Number of threads per computing node, give 0 if unsure	yes	standard
cavgseoproc_nano	Number of threads per computing node, give 0 if unsure	yes	standard
cavgsproc_nano	Number of threads per computing node, give 0 if unsure	yes	standard
center	Number of threads per computing node, give 0 if unsure	yes	standard
center2D_nano	Number of threads per computing node, give 0 if unsure	yes	standard
check_refpick	Number of threads per computing node, give 0 if unsure	yes	standard
cls_split	Number of threads per computing node, give 0 if unsure	yes	standard
cluster2D_nano	Number of threads per computing node, give 0 if unsure	yes	standard
cluster_cavgs	Number of threads per computing node, give 0 if unsure	yes	standard
cluster_cavgs_selection	Number of threads per computing node, give 0 if unsure	yes	standard
cluster_stack	Number of threads per computing node, give 0 if unsure	yes	standard
conv_atom_denoise	Number of threads per computing node, give 0 if unsure	yes	standard
crys_score	Number of threads per computing node, give 0 if unsure	yes	standard
ctf_correct	Number of threads per computing node, give 0 if unsure	yes	standard
ctf_estimate	Number of threads per computing node, give 0 if unsure	yes	standard
ctfops	Number of threads per computing node, give 0 if unsure	yes	standard
denoise_project	Number of threads per computing node, give 0 if unsure	yes	standard
detect_atoms	Number of threads per computing node, give 0 if unsure	yes	standard
dock_volpair	Number of threads per computing node, give 0 if unsure	yes	standard
estimate_diam	Number of threads per computing node, give 0 if unsure	yes	standard
extract	Number of threads per computing node, give 0 if unsure	yes	standard
filter	Number of threads per computing node, give 0 if unsure	yes	standard
flex_analysis	Number of threads per computing node, give 0 if unsure	yes	standard
fractionate_movies	Number of threads per computing node, give 0 if unsure	yes	standard
fsc	Number of threads per computing node, give 0 if unsure	yes	standard
fsc_area_score	Number of threads per computing node, give 0 if unsure	yes	standard
gen_pickrefs	Number of threads per computing node, give 0 if unsure	yes	standard
gen_pspecs_and_thumbs	Number of threads per computing node, give 0 if unsure	yes	standard
graphene_subtr	Number of threads per computing node, give 0 if unsure	yes	standard
icm2D	Number of threads per computing node, give 0 if unsure	yes	standard
icm3D	Number of threads per computing node, give 0 if unsure	yes	standard
make_cavgs	Number of threads per computing node, give 0 if unsure	yes	standard
make_oris	Number of threads per computing node, give 0 if unsure	yes	standard
mask	Number of threads per computing node, give 0 if unsure	yes	standard
match_cavgs	Number of threads per computing node, give 0 if unsure	yes	standard
match_stacks	Number of threads per computing node, give 0 if unsure	yes	standard
mini_stream	Number of threads per computing node, give 0 if unsure	yes	standard
model_cavgs_rejection	Number of threads per computing node, give 0 if unsure	yes	standard
motion_correct	Number of threads per computing node, give 0 if unsure	yes	standard
normalize	Number of threads per computing node, give 0 if unsure	yes	standard
nu_filt3D	Number of threads per computing node, give 0 if unsure	yes	standard
oristats	Number of threads per computing node, give 0 if unsure	yes	standard
particle_sieving	Number of threads per computing node, give 0 if unsure	yes	standard
pick	Number of threads per computing node, give 0 if unsure	yes	standard
pick_extract	Number of threads per computing node, give 0 if unsure	yes	standard
postprocess	Number of threads per computing node, give 0 if unsure	yes	standard
ppca_denoise	Number of threads per computing node, give 0 if unsure	yes	standard
ppca_denoise_classes	Number of threads per computing node, give 0 if unsure	yes	standard
ppca_volvar	Number of threads per computing node, give 0 if unsure	yes	standard
preproc	Number of threads per computing node, give 0 if unsure	yes	standard
preprocess	Number of threads per computing node, give 0 if unsure	yes	standard
ptclsproc_nano	Number of threads per computing node, give 0 if unsure	yes	standard
reconstruct3D	Number of threads per computing node, give 0 if unsure	yes	standard
reconstruct3D_pcg	Number of threads per computing node, give 0 if unsure	yes	standard
reextract	Number of threads per computing node, give 0 if unsure	yes	standard
refine3D	Number of threads per computing node, give 0 if unsure	yes	standard
refine3D_auto	Number of threads per computing node, give 0 if unsure	yes	standard
refine3D_multi	Number of threads per computing node, give 0 if unsure	yes	standard
refine3D_nano	Number of threads per computing node, give 0 if unsure	yes	standard
reproject	Number of threads per computing node, give 0 if unsure	yes	standard
sample_classes	Number of threads per computing node, give 0 if unsure	yes	standard
scale	Number of threads per computing node, give 0 if unsure	yes	standard
sieve_cavgs	Number of threads per computing node, give 0 if unsure	yes	standard
simulate_movie	Number of threads per computing node, give 0 if unsure	yes	standard
simulate_nanoparticle	Number of threads per computing node, give 0 if unsure	yes	standard
simulate_particles	Number of threads per computing node, give 0 if unsure	yes	standard
stackops	Number of threads per computing node, give 0 if unsure	yes	standard
symaxis_search	Number of threads per computing node, give 0 if unsure	yes	standard
symmetrize_map	Number of threads per computing node, give 0 if unsure	yes	standard
symmetry_test	Number of threads per computing node, give 0 if unsure	yes	standard
track_particles	Number of threads per computing node, give 0 if unsure	yes	standard
trajectory_denoise	Number of threads per computing node, give 0 if unsure	yes	standard
trajectory_make_projavgs	Number of threads per computing node, give 0 if unsure	yes	standard
trajectory_reconstruct3D	Number of threads per computing node, give 0 if unsure	yes	standard
tseries_extractor	Number of threads per computing node, give 0 if unsure	yes	standard
tseries_make_pickavg	Number of threads per computing node, give 0 if unsure	yes	standard
tseries_motion_correct	Number of threads per computing node, give 0 if unsure	yes	standard
tseries_prep4tracking	Number of threads per computing node, give 0 if unsure	yes	standard
uniform_filter2D	Number of threads per computing node, give 0 if unsure	yes	standard
uniform_filter3D	Number of threads per computing node, give 0 if unsure	yes	standard
validate_cavgs_vs_model	Number of threads per computing node, give 0 if unsure	yes	standard
volanalyze	Number of threads per computing node, give 0 if unsure	yes	standard
volcluster	Number of threads per computing node, give 0 if unsure	no	advanced
volops	Number of threads per computing node, give 0 if unsure	yes	standard

Parameter nthr_ini3D

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Number of threads for ini3D phase, give 0 if unsure	no	standard

Parameter nu_refine

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D	NU resolution expansion refinement	no	advanced
refine3D_auto	NU resolution expansion refinement	no	advanced

Parameter numlen

Used by program	Parameter label	Required in this program	Parameter visibility
preprocess	Length of number string	no	advanced

Parameter nxpatch

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	# of patches along x-axis	no	advanced
preprocess	# of patches along x-axis	no	advanced
tseries_make_pickavg	# of patches along x-axis	no	advanced
tseries_motion_correct	# of patches along x-axis	no	advanced

Parameter nypatch

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	# of patches along y-axis	no	advanced
preprocess	# of patches along y-axis	no	advanced
tseries_make_pickavg	# of patches along y-axis	no	advanced
tseries_motion_correct	# of patches along y-axis	no	advanced

Parameter objfun

Used by program	Parameter label	Required in this program	Parameter visibility
reconstruct3D_pcg	Objective function	no	developer
refine3D	Objective function	no	advanced

Parameter objfun_den

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Denoised objective	no	advanced
refine3D	Denoised objective	no	advanced

Parameter objfun_den_w

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Denoised objective weight	no	advanced
refine3D	Denoised objective weight	no	advanced

Parameter offset

Used by program	Parameter label	Required in this program	Parameter visibility
track_particles	Shift half-width search bound	no	advanced

Parameter optics_dir

Used by program	Parameter label	Required in this program	Parameter visibility
gen_pickrefs	Target directory for optics import	no	advanced

Parameter optics_offset

Used by program	Parameter label	Required in this program	Parameter visibility
assign_optics_groups	Numbering offset to apply to optics groups	no	developer
export_relion	Offset to apply to optics group numbering	no	developer

Parameter oritab

Used by program	Parameter label	Required in this program	Parameter visibility
center	Orientation and CTF parameter file	no	developer
ctfops	Orientation and CTF parameter file	no	advanced
import_particles	Orientation and CTF parameter file	no	advanced
mask	Orientation and CTF parameter file	no	advanced
oriops	Orientation and CTF parameter file	yes	standard
oristats	Orientation and CTF parameter file	yes	standard
reproject	Orientation and CTF parameter file	no	advanced
simulate_particles	Orientation and CTF parameter file	no	advanced
stackops	Orientation and CTF parameter file	no	advanced
vizoris	Orientation and CTF parameter file	yes	standard

Parameter oritab2

Used by program	Parameter label	Required in this program	Parameter visibility
oristats	2nd orientation and CTF parameter file	no	developer

Parameter oritype

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Particle type to split	no	advanced
flex_analysis	Particle orientation segment	no	advanced
make_oris	Oritype segment in project	no	developer
oriops	Oritype segment in project	no	developer
oristats	Oritype segment in project	no	developer
print_project_field	Oritype segment in project	yes	standard
reconstruct3D_pcg	Oritype segment in project	no	developer
reextract	Oritype segment in project	no	advanced
replace_project_field	Oritype segment in project	yes	standard
selection	Oritype segment in project	no	advanced
vizoris	Oritype segment in project	no	advanced

Parameter osmpl_fac

Used by program	Parameter label	Required in this program	Parameter visibility
bootstrap_cavgs	Oversampling factor	no	developer

Parameter outfile

Used by program	Parameter label	Required in this program	Parameter visibility
bootstrap_rec3D	Resolution output prefix	no	developer
center	Output orientation and CTF parameter file	no	developer
dock_volpair	Output orientation and CTF parameter file	no	advanced
flex_analysis	Discrete-state project	no	advanced
make_oris	Output orientation and CTF parameter file	no	developer
mask	Output orientation and CTF parameter file	no	advanced
oriops	Output orientation and CTF parameter file	no	developer
simulate_particles	Output orientation and CTF parameter file	no	advanced
stackops	Output orientation and CTF parameter file	no	advanced
volcluster	Output orientation and CTF parameter file	no	advanced
volops	Output orientation and CTF parameter file	no	advanced

Parameter outside

Used by program	Parameter label	Required in this program	Parameter visibility
extract	Extract outside stage boundaries	no	advanced
reextract	Extract outside stage boundaries	no	advanced

Parameter outstk

Used by program	Parameter label	Required in this program	Parameter visibility
convert	Output stack name	no	advanced
ctfops	Output stack name	no	advanced
filter	Output stack name	no	advanced
graphene_subtr	Output stack name	no	advanced
ppca_denoise	Output stack name	no	advanced
reproject	Output stack name	no	advanced
scale	Output stack name	no	advanced
simulate_particles	Output stack name	no	advanced
stack	Output stack name	no	advanced
stackops	Output stack name	no	advanced
trajectory_denoise	Output stack name	no	advanced

Parameter outvol

Used by program	Parameter label	Required in this program	Parameter visibility
convert	Output volume name	no	advanced
dock_volpair	Output volume name	no	advanced
filter	Output volume name	no	advanced
flex_analysis	Output volume name	no	advanced
nu_filt3D	Output volume name	no	advanced
pdb2mrc	Output volume name	no	advanced
scale	Output volume name	no	advanced
simulate_nanoparticle	Output volume name	no	advanced
symmetrize_map	Output volume name	no	advanced
volops	Output volume name	no	advanced

Parameter particle_density

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Particle density in micrographs	no	developer
pick	Particle density in micrographs	no	advanced

Parameter pca_mode

Used by program	Parameter label	Required in this program	Parameter visibility
cls_split	Class split embedding method	no	advanced
ppca_denoise	PCA methods: PPCA, PPCA plus residual kPCA, standard SVD PCA, kernel PCA, or diffusion maps	no	advanced
ppca_denoise_classes	PCA methods: PPCA, standard SVD PCA or kernel PCA	no	advanced
trajectory_denoise	PCA methods: diffusion maps, PPCA, PPCA plus residual kPCA, standard SVD PCA, or kernel PCA	no	advanced

Parameter pcgop

Used by program	Parameter label	Required in this program	Parameter visibility
reconstruct3D_pcg	PCG normal operator	no	developer

Parameter pcontrast

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Input particle contrast	no	developer
extract	Input particle contrast	no	standard
mini_stream	Input particle contrast	no	advanced
pick	Input particle contrast	no	advanced
pick_extract	Input particle contrast	no	advanced
reextract	Input particle contrast	no	advanced

Parameter pdbfile

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_stats	PDB	yes	standard
mask	PDB for 3D envelope masking	no	advanced
model_validate	PDB input coordinates file	yes	standard
pdb2mrc	PDB input coordinates file	yes	standard
simulate_nanoparticle	PDB	no	advanced

Parameter pdbfile2

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_stats	PDB	no	advanced

Parameter pdbfiles

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_rmsd	txt	yes	standard
core_atoms_analysis	txt	yes	standard

Parameter pdbout

Used by program	Parameter label	Required in this program	Parameter visibility
pdb2mrc	Output PDB volume-centered molecule	no	advanced

Parameter period

Used by program	Parameter label	Required in this program	Parameter visibility
tseries_make_pickavg	Period for repeated averaging windows	no	advanced

Parameter pgrp

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Point-group symmetry	yes	standard
abinitio3D_cavgs	Point-group symmetry	yes	standard
autorefine3D_nano	Point-group symmetry	yes	standard
bootstrap_rec3D	Point-group symmetry	yes	standard
cavgseoproc_nano	Point-group symmetry	yes	standard
cavgsproc_nano	Point-group symmetry	yes	standard
make_oris	Point-group symmetry	no	developer
oriops	Point-group symmetry	no	developer
oristats	Point-group symmetry	no	developer
pick_extract	Point-group symmetry	no	standard
ptclsproc_nano	Point-group symmetry	yes	standard
reconstruct3D	Point-group symmetry	yes	standard
refine3D	Point-group symmetry	yes	standard
refine3D_auto	Point-group symmetry	yes	standard
refine3D_multi	Point-group symmetry	yes	standard
refine3D_nano	Point-group symmetry	yes	standard
reproject	Point-group symmetry	yes	standard
simulate_particles	Point-group symmetry	yes	standard
symaxis_search	Point-group symmetry	yes	standard
symmetrize_map	Point-group symmetry	yes	standard
trajectory_reconstruct3D	Point-group symmetry	yes	standard
validate_cavgs_vs_model	Point-group symmetry	yes	standard
vizoris	Point-group symmetry	yes	standard

Parameter pgrp_start

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Initital point-group symmetry	no	advanced
abinitio3D_cavgs	Initital point-group symmetry	no	advanced

Parameter phrand

Used by program	Parameter label	Required in this program	Parameter visibility
filter	Phase randomization	no	advanced

Parameter phshift_max

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Maximum CTF phase shift	no	developer
ctf_estimate	Maximum CTF phase shift	no	advanced
mini_stream	Maximum CTF phase shift	no	advanced
preproc	Maximum CTF phase shift	no	developer
preprocess	Maximum CTF phase shift	no	advanced

Parameter phshift_min

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Minimum CTF phase shift	no	developer
ctf_estimate	Minimum CTF phase shift	no	advanced
mini_stream	Minimum CTF phase shift	no	advanced
preproc	Minimum CTF phase shift	no	developer
preprocess	Minimum CTF phase shift	no	advanced

Parameter phshift_step

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	CTF phase-shift step	no	developer
ctf_estimate	CTF phase-shift step	no	advanced
mini_stream	CTF phase-shift step	no	advanced
preproc	CTF phase-shift step	no	developer
preprocess	CTF phase-shift step	no	advanced

Parameter phshiftunit

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	Phase-shift unit	no	advanced

Parameter pick_roi

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Artefactual regions exclusion(new picker only)	no	developer
pick	Artefactual regions exclusion(new picker only)	no	advanced

Parameter picker

Used by program	Parameter label	Required in this program	Parameter visibility
pick	Which picker to use	no	advanced

Parameter pickrefs

Used by program	Parameter label	Required in this program	Parameter visibility
check_refpick	Stack of class-averages/reprojections for picking	yes	standard
master	2D averages for use as picking references (optional)	no	developer
pick	Stack of class-averages/reprojections for picking	no	standard
pick_extract	Stack of class-averages/reprojections for picking	no	standard

Parameter plaintexttab

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	Plain text file of input parameters	no	advanced

Parameter platonic

Used by program	Parameter label	Required in this program	Parameter visibility
symmetry_test	Search for Platonic symmetries	no	advanced

Parameter plot_key

Used by program	Parameter label	Required in this program	Parameter visibility
print_project_field	plot plot_key on , sort on x	no	developer

Parameter positive

Used by program	Parameter label	Required in this program	Parameter visibility
automask2D	Consider only positive pixels	no	advanced

Parameter postprocess

Used by program	Parameter label	Required in this program	Parameter visibility
bootstrap_rec3D	Postprocess final map	no	developer
reconstruct3D	Postprocess final map	no	advanced

Parameter ppca_kpca_resid_alpha

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise	Residual hybrid damping (0 => PPCA only; default 0.5)	no	advanced
trajectory_denoise	Residual hybrid damping (0 => PPCA only; default 0.5)	no	advanced

Parameter pre_norm

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise_classes	Pre-normalize images	no	advanced

Parameter preimage_mode

Used by program	Parameter label	Required in this program	Parameter visibility
flex_analysis	Diffusion-map output mode	no	advanced

Parameter preimage_ndim

Used by program	Parameter label	Required in this program	Parameter visibility
flex_analysis	Local-linear pre-image design dimension (default 2)	no	advanced

Parameter prob_neigh_mode

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D	Prob-neigh neighborhood mode	no	advanced
refine3D_multi	Prob-neigh neighborhood mode	no	advanced

Parameter projfile

Used by program	Parameter label	Required in this program	Parameter visibility
estimate_lpstages	Project file	yes	standard
export_manifoldem_starproject	Project file	yes	standard
extract_subproj	Project file	yes	standard
extract_substk	Project file	yes	standard
map_params_from_den	Project file	no	advanced
match_cavgs	Project file	yes	standard
new_project	Project file	no	advanced
ptcl3D_state_consensus	Project file	yes	standard
replace_project_field	Project file	yes	standard
scale	Project file	no	advanced
selection	Project file	yes	standard
update_project	Project file	yes	standard
validate_projfile	Project file	yes	standard
write_mic_filetab	Project file	yes	standard

Parameter projfile_den

Used by program	Parameter label	Required in this program	Parameter visibility
map_params_from_den	Denoised child project file	yes	standard

Parameter projfile_merged

Used by program	Parameter label	Required in this program	Parameter visibility
merge_projects	Merged output project file	yes	standard

Parameter projfile_orig

Used by program	Parameter label	Required in this program	Parameter visibility
unbootstrap_cavgs	Original project file	yes	standard

Parameter projfile_raw

Used by program	Parameter label	Required in this program	Parameter visibility
map_params_from_den	Raw project file	yes	standard

Parameter projfile_ref

Used by program	Parameter label	Required in this program	Parameter visibility
match_cavgs	Reference project file	yes	standard

Parameter projfile_target

Used by program	Parameter label	Required in this program	Parameter visibility
replace_project_field	Another project file	yes	standard

Parameter projname

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Project name	no	advanced

Parameter projrec

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Projection-direction reconstruction	no	advanced
reconstruct3D	Projection-direction reconstruction	no	advanced
refine3D	Projection-direction reconstruction	no	advanced

Parameter projstats

Used by program	Parameter label	Required in this program	Parameter visibility
oristats	Projection statistics	no	developer

Parameter projtab

Used by program	Parameter label	Required in this program	Parameter visibility
merge_projects	Project file table	yes	standard
ptcl3D_state_consensus	Project file table	yes	standard

Parameter prune

Used by program	Parameter label	Required in this program	Parameter visibility
cluster_cavgs	Automated particles pruning	no	advanced
map_cavgs_selection	Automated particles pruning	no	advanced
match_cavgs	Automated particles pruning	no	developer
model_cavgs_rejection	Automated particles pruning	no	advanced
ptcl3D_state_consensus	Automated particles pruning	no	advanced
select_clusters	Automated particles pruning	no	developer
selection	Automated particles pruning	no	advanced

Parameter pspecsz

Used by program	Parameter label	Required in this program	Parameter visibility
ctf_estimate	Size of power spectrum	no	advanced
gen_pspecs_and_thumbs	Size of power spectrum	no	developer
motion_correct	Size of power spectrum	no	advanced
preprocess	Size of power spectrum	no	advanced

Parameter ptcl_src

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Particle source	no	advanced
reconstruct3D	Particle source	no	advanced
refine3D	Particle source	no	advanced
refine3D_auto	Particle source	no	advanced
refine3D_multi	Particle source	no	advanced

Parameter qsys_name

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Queue system kind	no	advanced
update_project	Queue system kind	no	advanced

Parameter qsys_partition

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Name of SLURM/PBS/LSF partition	no	advanced
update_project	Name of SLURM/PBS/LSF partition	no	advanced

Parameter qsys_qos

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Schedule priority	no	advanced
update_project	Schedule priority	no	advanced

Parameter qsys_reservation

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Name of reserved partition	no	advanced
update_project	Name of reserved partition	no	advanced

Parameter quality_context

Used by program	Parameter label	Required in this program	Parameter visibility
model_cavgs_rejection	Class-average quality context	no	advanced

Parameter quality_mode

Used by program	Parameter label	Required in this program	Parameter visibility
model_cavgs_rejection	Class-average quality mode	no	advanced

Parameter quality_model

Used by program	Parameter label	Required in this program	Parameter visibility
model_cavgs_rejection	Class-average quality model	no	advanced

Parameter real_filter

Used by program	Parameter label	Required in this program	Parameter visibility
filter	Real-space filter	no	advanced

Parameter ref_ind

Used by program	Parameter label	Required in this program	Parameter visibility
volanalyze	Reference volume index	no	advanced

Parameter refine

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Refinement mode	no	advanced
abinitio2D_chunks	Refinement mode	no	advanced
refine3D	Refinement mode	no	advanced

Parameter refs

Used by program	Parameter label	Required in this program	Parameter visibility
make_cavgs	Output 2D references	no	advanced
particle_sieving	Reference class averages to initialise size compatibility model	no	advanced

Parameter reliongroups

Used by program	Parameter label	Required in this program	Parameter visibility
export_relion	Number of Relion groups based on defocus	no	developer

Parameter remap_cls

Used by program	Parameter label	Required in this program	Parameter visibility
make_cavgs	Whether to remap 2D clusters	no	advanced

Parameter res_target

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D_auto	Resolution target (in A)	no	advanced

Parameter res_threshold

Used by program	Parameter label	Required in this program	Parameter visibility
selection	Class resolution threshold	no	advanced

Parameter rmsd_file

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_stats	bin	no	advanced

Parameter roavg

Used by program	Parameter label	Required in this program	Parameter visibility
estimate_diam	Rotationally average	no	advanced
stackops	Rotationally average	no	advanced

Parameter rtol

Used by program	Parameter label	Required in this program	Parameter visibility
reconstruct3D_pcg	PCG relative residual tolerance	no	developer

Parameter scale

Used by program	Parameter label	Required in this program	Parameter visibility
scale	Scaling ratio	no	advanced

Parameter script

Used by program	Parameter label	Required in this program	Parameter visibility
analysis2D_nano	Generate script for shared-mem exec on cluster	no	advanced
autorefine3D_nano	Generate script for shared-mem exec on cluster	no	advanced
cavgseoproc_nano	Generate script for shared-mem exec on cluster	no	developer
cavgsproc_nano	Generate script for shared-mem exec on cluster	no	developer
center2D_nano	Generate script for shared-mem exec on cluster	no	advanced
cluster2D_nano	Generate script for shared-mem exec on cluster	no	advanced
ptclsproc_nano	Generate script for shared-mem exec on cluster	no	developer
validate_cavgs_vs_model	Generate script for shared-mem exec on cluster	no	developer

Parameter select_flag

Used by program	Parameter label	Required in this program	Parameter visibility
select_clusters	flag to use for selection	no	developer

Parameter sherr

Used by program	Parameter label	Required in this program	Parameter visibility
make_oris	Shift error half-width	no	developer
oriops	Shift error half-width	no	developer
simulate_particles	Shift error half-width	no	advanced

Parameter sigma

Used by program	Parameter label	Required in this program	Parameter visibility
filter	sigma, for Gaussian generation	no	advanced

Parameter sigma_est

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D	Sigma estimation method	no	advanced
refine3D	Sigma estimation method	no	advanced

Parameter single_pass

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Coarse pass only	no	advanced

Parameter skip_rejection

Used by program	Parameter label	Required in this program	Parameter visibility
cluster_cavgs	Skip class-average rejection	no	advanced

Parameter smpd

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_rmsd	Sampling distance	yes	standard
atoms_stats	Sampling distance	yes	standard
auto_spher_mask	Sampling distance	yes	standard
automask	Sampling distance	yes	standard
automask2D	Sampling distance	yes	standard
autorefine3D_nano	Sampling distance	yes	standard
cavgseoproc_nano	Sampling distance	yes	standard
cavgsproc_nano	Sampling distance	yes	standard
center	Sampling distance	yes	standard
check_refpick	Sampling distance	yes	standard
cif2mrc	Sampling distance	no	advanced
conv_atom_denoise	Sampling distance	yes	standard
core_atoms_analysis	Sampling distance	yes	standard
crys_score	Sampling distance	yes	standard
ctf_correct	Sampling distance	yes	standard
ctfops	Sampling distance	yes	standard
detect_atoms	Sampling distance	yes	standard
dock_volpair	Sampling distance	yes	standard
estimate_diam	Sampling distance	yes	standard
filter	Sampling distance	yes	standard
fsc	Sampling distance	yes	standard
fsc_area_score	Sampling distance	yes	standard
graphene_subtr	Sampling distance	yes	standard
icm2D	Sampling distance	yes	standard
icm3D	Sampling distance	yes	standard
import_cavgs	Sampling distance	yes	standard
import_movies	Sampling distance	yes	standard
import_particles	Sampling distance	yes	standard
import_trajectory	Sampling distance	yes	standard
mask	Sampling distance	yes	standard
master	Pixel size (A)	yes	standard
mini_stream	Sampling distance	yes	standard
model_validate	Sampling distance	yes	standard
noisevol	Sampling distance	yes	standard
normalize	Sampling distance	yes	standard
nu_filt3D	Sampling distance	yes	standard
pdb2mrc	Sampling distance	no	advanced
ppca_denoise	Sampling distance	yes	standard
ppca_volvar	Sampling distance	yes	standard
preproc	Sampling distance	yes	standard
print_dose_weights	Sampling distance	yes	standard
print_fsc	Sampling distance	no	advanced
print_magic_boxes	Sampling distance	yes	standard
ptclsproc_nano	Sampling distance	yes	standard
reproject	Sampling distance	yes	standard
scale	Sampling distance	yes	standard
simulate_movie	Sampling distance	yes	standard
simulate_nanoparticle	Sampling distance	yes	standard
simulate_particles	Sampling distance	yes	standard
split	Sampling distance	yes	standard
stack	Sampling distance	yes	standard
stackops	Sampling distance	yes	standard
symaxis_search	Sampling distance	yes	standard
symmetrize_map	Sampling distance	yes	standard
symmetry_test	Sampling distance	yes	standard
trajectory_denoise	Sampling distance	yes	standard
tsegmaps_core_finder	Sampling distance	yes	standard
tseries_import	Sampling distance	yes	standard
uniform_filter2D	Sampling distance	yes	standard
uniform_filter3D	Sampling distance	yes	standard
validate_cavgs_vs_model	Sampling distance	yes	standard
volanalyze	Sampling distance	yes	standard
volcluster	Sampling distance	yes	standard
volops	Sampling distance	no	advanced

Parameter smpd_downscale

Used by program	Parameter label	Required in this program	Parameter visibility
master	Downscaled pixel size (A)	no	developer
motion_correct	Sampling distance after downscale	no	advanced
preproc	Sampling distance after downscale	no	standard
preprocess	Sampling distance after downscale	no	advanced

Parameter smpd_target

Used by program	Parameter label	Required in this program	Parameter visibility
model_validate	Target sampling distance	yes	standard

Parameter snr

Used by program	Parameter label	Required in this program	Parameter visibility
simulate_movie	SNR	no	advanced
simulate_particles	SNR	yes	standard
stackops	Apply noise to give SNR	no	advanced
volops	SNR	no	advanced

Parameter sort

Used by program	Parameter label	Required in this program	Parameter visibility
print_project_field	sort oris on key	no	developer

Parameter starfile

Used by program	Parameter label	Required in this program	Parameter visibility
export_manifoldem_starproject	STAR-format file name	no	developer
import_particles	Particles Metadata starfile	no	standard
import_starproject	Metadata starfile	no	standard

Parameter state

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Continuation state label	no	advanced
extract_substk	State index	no	advanced
oriops	State to modify	no	developer
postprocess	State to postprocess	no	advanced
prune_project	State index	no	developer
reconstruct3D_pcg	State to reconstruct	no	developer
selection	State number	no	advanced
stackops	State index	no	advanced

Parameter stats

Used by program	Parameter label	Required in this program	Parameter visibility
info_image	Output statistics	no	advanced
stackops	Provide statistics	no	advanced

Parameter stepsz

Used by program	Parameter label	Required in this program	Parameter visibility
trajectory_reconstruct3D	Time window size (# frames){500}	no	developer

Parameter stk

Used by program	Parameter label	Required in this program	Parameter visibility
automask2D	Particle image stack	yes	standard
binarize	Stack	no	developer
center	Particle image stack	no	developer
cluster_cavgs	Particle image stack	no	advanced
cluster_stack	Particle image stack	yes	standard
convert	Stack	no	advanced
ctfops	Particle image stack	no	advanced
estimate_diam	Particle image stack	yes	standard
filter	Stack to filter	no	advanced
icm2D	Odd stack	yes	standard
import_cavgs	Stack of class averages	yes	standard
import_particles	Stack of particles	no	advanced
import_trajectory	Particle image stack	yes	standard
map_cavgs_selection	Stack of cavgs to select from	no	advanced
mask	Particle image stack	no	advanced
match_stacks	Particle image stack	yes	standard
normalize	Stack to normalize	no	advanced
ppca_denoise	Stack to denoise	yes	standard
reimport_particles	Denoised particle stack	yes	standard
scale	Particle image stack	no	advanced
simulate_movie	Particle image stack	no	advanced
split	Particle image stack	yes	standard
stackops	Particle image stack	yes	standard
trajectory_denoise	Stack to denoise	yes	standard
trajectory_swap_stack	Particle image stack	yes	standard
uniform_filter2D	Odd stack	yes	standard

Parameter stk2

Used by program	Parameter label	Required in this program	Parameter visibility
icm2D	Even stack	yes	standard
map_cavgs_selection	Stack of selected cavgs	yes	standard
match_stacks	Second Particle image stack	yes	standard
uniform_filter2D	Even stack	yes	standard

Parameter stk_backgr

Used by program	Parameter label	Required in this program	Parameter visibility
graphene_subtr	background power spectra stack, eg NP_X_background_pspec.mrc	yes	standard

Parameter stk_den

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	Denoised particle image stack	no	advanced

Parameter stk_traj

Used by program	Parameter label	Required in this program	Parameter visibility
graphene_subtr	Tracked NP image stack	yes	standard

Parameter stktab

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	List of per-micrograph particle stacks	no	advanced
info_stktab	List of per-micrograph particle stacks	yes	standard

Parameter stktab_den

Used by program	Parameter label	Required in this program	Parameter visibility
import_particles	List of denoised particle stacks	no	advanced

Parameter subprojname

Used by program	Parameter label	Required in this program	Parameter visibility
extract_subproj	Subproject name	yes	standard

Parameter symrnd

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Randomize over subgroubs of point-group	no	developer

Parameter taper_edges

Used by program	Parameter label	Required in this program	Parameter visibility
mask	Taper edges	no	advanced

Parameter tester

Used by program	Parameter label	Required in this program	Parameter visibility
track_particles	Write periodic tester-mode outputs	no	advanced

Parameter thres

Used by program	Parameter label	Required in this program	Parameter visibility
automask	Volume threshold	no	advanced
master	Distance threshold for peak picking(A)	no	developer

Parameter tilt_thres

Used by program	Parameter label	Required in this program	Parameter visibility
assign_optics_groups	Threshold for hierarchical clustering of beamtilts	no	developer
export_relion	Distance threshold	no	developer
preproc	Threshold for hierarchical clustering of beamtilts	no	developer

Parameter tiltgroupmax

Used by program	Parameter label	Required in this program	Parameter visibility
export_relion	Max movies in a tilt/optics group	no	developer

Parameter time_per_image

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Time per image	no	advanced
update_project	Time per image	no	advanced

Parameter tof

Used by program	Parameter label	Required in this program	Parameter visibility
fractionate_movies	Final frame	no	advanced

Parameter top

Used by program	Parameter label	Required in this program	Parameter visibility
extract_subproj	To index	no	advanced
extract_substk	To index	no	advanced
scale	Last stack index	no	advanced
stackops	To particle index	no	advanced
trajectory_reconstruct3D	To particle index	no	developer

Parameter total_dose

Used by program	Parameter label	Required in this program	Parameter visibility
master	Total exposure dose (e/A2)	yes	standard
motion_correct	Total exposure dose (e/Ang^2)	no	standard
preproc	Total exposure dose (e/Ang^2)	no	standard
preprocess	Total exposure dose (e/Ang^2)	no	advanced
print_dose_weights	Total exposure dose (e/Ang^2)	yes	standard

Parameter transp_pca

Used by program	Parameter label	Required in this program	Parameter visibility
ppca_denoise_classes	transpose for pixel-wise learning	no	advanced

Parameter trs

Used by program	Parameter label	Required in this program	Parameter visibility
autorefine3D_nano	Maximum translational shift	no	advanced
center2D_nano	Maximum translational shift	no	advanced
cluster2D_nano	Maximum translational shift	no	advanced
dock_volpair	Maximum translational shift	no	advanced
motion_correct	Max shift per iter in pixels{10.}	no	advanced
preprocess	Max shift per iter in pixels{10.}	no	advanced
refine3D	Maximum translational shift	no	advanced
refine3D_nano	Maximum translational shift	no	advanced
simulate_movie	Maximum translational shift	no	advanced
tseries_make_pickavg	Max shift per iter in pixels{10.}	no	advanced
tseries_motion_correct	Max shift per iter in pixels{10.}	no	advanced

Parameter trsstats

Used by program	Parameter label	Required in this program	Parameter visibility
oristats	Shift statistics	no	developer

Parameter tseries

Used by program	Parameter label	Required in this program	Parameter visibility
vizoris	Time series analysis	no	advanced

Parameter update_frac

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D	Fractional update per iteration	no	advanced
refine3D_nano	Fractional update per iteration	no	advanced

Parameter use_model

Used by program	Parameter label	Required in this program	Parameter visibility
particle_sieving	Use model for class-average rejection in sieving	no	advanced

Parameter user_account

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	User account name in SLURM/PBS/LSF	no	advanced
update_project	User account name in SLURM/PBS/LSF	no	advanced

Parameter user_email

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	Your e-mail address	no	advanced
update_project	Your e-mail address	no	advanced

Parameter user_project

Used by program	Parameter label	Required in this program	Parameter visibility
new_project	User project name in SLURM/PBS/LSF	no	advanced
update_project	User project name in SLURM/PBS/LSF	no	advanced

Parameter view_balance

Used by program	Parameter label	Required in this program	Parameter visibility
flex_analysis	Correct uneven view distribution	no	advanced

Parameter vis

Used by program	Parameter label	Required in this program	Parameter visibility
info_image	Visualize image	no	advanced
stackops	Visualize stack images	no	advanced

Parameter vol1

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio3D	Starting template volume	no	advanced
atoms_stats	Raw volume	yes	standard
auto_spher_mask	Odd volume	yes	standard
automask	Odd volume	yes	standard
autorefine3D_nano	FCC reference volume	yes	standard
binarize	Volume	no	developer
cavgseoproc_nano	Volume	yes	standard
cavgsproc_nano	Volume	yes	standard
center	Volume	no	developer
conv_atom_denoise	Volume	yes	standard
convert	Volume	no	advanced
detect_atoms	Volume	yes	standard
dock_volpair	Volume	yes	standard
filter	Volume to filter	no	advanced
flex_analysis	Mean volume	yes	standard
fsc	Odd volume	yes	standard
fsc_area_score	Odd volume	yes	standard
icm3D	Odd volume	yes	standard
mask	Volume	no	advanced
model_validate	Experimental volume	yes	standard
normalize	Volume to normalize	no	advanced
nu_filt3D	Odd volume	yes	standard
postprocess	Volume override	no	advanced
ppca_volvar	Volume	yes	standard
refine3D	Reference volume	no	advanced
refine3D_auto	Starting template volume	no	advanced
refine3D_nano	FCC reference volume	no	advanced
reproject	Volume	yes	standard
scale	Input volume	no	advanced
simulate_particles	Volume	yes	standard
symaxis_search	C1 Volume to identify symmetry axis of	yes	standard
symmetrize_map	Volume to symmetrize	yes	standard
symmetry_test	C1 Volume to identify symmetry of	yes	standard
trajectory_reconstruct3D	Mean volume for latent chunking	no	developer
uniform_filter3D	Odd volume	yes	standard
validate_cavgs_vs_model	Volume	yes	standard
volops	Volume	yes	standard

Parameter vol2

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_stats	Connected components volume	yes	standard
automask	Even volume	yes	standard
dock_volpair	Volume	yes	standard
fsc	Even volume	yes	standard
fsc_area_score	Even volume	yes	standard
icm3D	Even volume	yes	standard
nu_filt3D	Even volume	yes	standard
uniform_filter3D	Even volume	yes	standard

Parameter vol3

Used by program	Parameter label	Required in this program	Parameter visibility
atoms_stats	Volume	no	advanced

Parameter vol_dim

Used by program	Parameter label	Required in this program	Parameter visibility
pdb2mrc	Simulated volume dimensions	no	advanced

Parameter vol_even

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D_nano	Even volume	no	advanced

Parameter vol_odd

Used by program	Parameter label	Required in this program	Parameter visibility
refine3D_nano	Odd volume	no	advanced

Parameter walltime

Used by program	Parameter label	Required in this program	Parameter visibility
abinitio2D_chunks	Walltime	no	advanced
abinitio2D_stream	Walltime	no	developer
new_project	Walltime	no	advanced
particle_sieving	Walltime	no	advanced
pick_extract	Walltime	no	advanced
preproc	Walltime	no	developer
sieve_cavgs	Walltime	no	advanced
update_project	Walltime	no	advanced

Parameter wcrit

Used by program	Parameter label	Required in this program	Parameter visibility
motion_correct	Correlation to weights conversion scheme	no	advanced
tseries_make_pickavg	Correlation to weights conversion scheme	no	advanced
tseries_motion_correct	Correlation to weights conversion scheme	no	advanced

Parameter which_iter

Used by program	Parameter label	Required in this program	Parameter visibility
bootstrap_rec3D	Sigma iteration index	no	developer

Parameter width

Used by program	Parameter label	Required in this program	Parameter visibility
filter	Cosine low-pass filter falloff	no	advanced
mask	Falloff of inner mask	no	advanced

Parameter winsz

Used by program	Parameter label	Required in this program	Parameter visibility
automask2D	Window size for median filter	no	advanced
binarize	Half-window size	no	developer
cluster2D_nano	Half-window size	no	advanced
filter	Half-window size	no	advanced
pick	Window size for sauvola	no	advanced
stackops	Window size for local sdev estimation	no	advanced

Parameter xdim

Used by program	Parameter label	Required in this program	Parameter visibility
simulate_movie	x-dimension	no	advanced

Parameter xmldir

Used by program	Parameter label	Required in this program	Parameter visibility
assign_optics_groups	Directory containing per movie EPU XML files	no	developer

Parameter xmlloc

Used by program	Parameter label	Required in this program	Parameter visibility
export_relion	Pathname of EPU XML files	no	developer

Parameter xsh

Used by program	Parameter label	Required in this program	Parameter visibility
volops	Translation along x-axis	no	advanced

Parameter ydim

Used by program	Parameter label	Required in this program	Parameter visibility
simulate_movie	y-dimension	no	advanced

Parameter ysh

Used by program	Parameter label	Required in this program	Parameter visibility
volops	Translation along y-axis	no	advanced

Parameter zero

Used by program	Parameter label	Required in this program	Parameter visibility
oriops	Zero shifts	no	developer

Parameter zsh

Used by program	Parameter label	Required in this program	Parameter visibility
volops	Translation along z-axis	no	advanced