UI Placeholder Review

This document inventories placeholder values by actual parameter key and program context. It is generated review evidence from the registered Fortran UI, not a source of runtime metadata. After review, apply approved wording to the owning Fortran descriptor and regenerate this inventory.

Registry source: /Users/elmlundho/src/SIMPLE/build/production/simple_private_exec prg=print_ui_json.

Each heading is one parameter key. Each row is a separate ui_program_input instance, so a key may have context-dependent wording. Edit Placeholder directly. Leave choice, binary, and hidden inputs empty unless the Fortran descriptor rule changes.

Inventory: 343 unique parameter keys and 1382 parameter instances.

Parameter acf

Used by program	Section	Type	Parameter label	Placeholder
stackops	parameter input/output	binary	Autocorrelation, A * conjg(A)	(empty)

Parameter algorithm

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	search controls	multi	Algorithm for motion correction	(empty)
preproc	parameter input/output	multi	Algorithm for motion correction	(empty)
preprocess	search controls	multi	Algorithm for motion correction	(empty)
tseries_motion_correct	search controls	multi	Algorithm for motion correction	(empty)

Parameter amsklp

Used by program	Section	Type	Parameter label	Placeholder
auto_spher_mask	filter controls	num	Low-pass limit for envelope mask generation	e.g. 10
automask	filter controls	num	Low-pass limit for envelope mask generation	e.g. 10
automask2D	filter controls	num	Low-pass limit for envelope mask generation	e.g. 10
estimate_diam	filter controls	num	Automask low-pass limit	e.g. 10
gen_pickrefs	filter controls	num	Automask low-pass limit	e.g. 10
refine3D	filter controls	num	Low-pass limit for envelope mask generation	e.g. 10
refine3D_auto	filter controls	num	Low-pass limit for envelope mask generation	e.g. 10

Parameter angastunit

Used by program	Section	Type	Parameter label	Placeholder
import_particles	parameter input/output	multi	Angle of astigmatism unit	(empty)

Parameter angerr

Used by program	Section	Type	Parameter label	Placeholder
make_oris	parameter input/output	num	Rotation angle error half-width	e.g. 10
oriops	parameter input/output	num	Rotation angle error half-width	e.g. 10

Parameter angstep

Used by program	Section	Type	Parameter label	Placeholder
stackops	parameter input/output	num	Angular stepsize	e.g. 10

Parameter append

Used by program	Section	Type	Parameter label	Placeholder
selection	parameter input/output	binary	Append selection to existing	(empty)

Parameter astigerr

Used by program	Section	Type	Parameter label	Placeholder
simulate_particles	parameter input/output	num	Astigmatism error	e.g. 10

Parameter astigthreshold

Used by program	Section	Type	Parameter label	Placeholder
pick_extract	filter controls	num	Astigmatism rejection threshold	e.g. 10

Parameter astigtol

Used by program	Section	Type	Parameter label	Placeholder
ctf_estimate	search controls	num	Expected astigmatism	e.g. 10
preprocess	search controls	num	Expected astigmatism	e.g. 10

Parameter athres

Used by program	Section	Type	Parameter label	Placeholder
fsc_area_score	parameter input/output	num	Cone half-angle	e.g. 10
trajectory_make_projavgs	parameter input/output	num	Angular threshold (degrees)	e.g. 10

Parameter automsk

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	mask controls	multi	Perform envelope masking	(empty)
automask	mask controls	multi	Perform envelope masking	(empty)
estimate_diam	mask controls	multi	Perform envelope masking	(empty)
fsc_area_score	mask controls	multi	Perform envelope masking	(empty)
nu_filt3D	mask controls	multi	Perform envelope masking	(empty)
refine3D	mask controls	multi	Perform envelope masking	(empty)
refine3D_auto	mask controls	multi	Perform envelope masking	(empty)
refine3D_multi	mask controls	multi	Perform envelope masking	(empty)

Parameter autoscale

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	binary	Automatic down-scaling	(empty)
refine3D_auto	search controls	binary	Automatic down-scaling	(empty)
refine3D_multi	search controls	binary	Automatic down-scaling	(empty)

Parameter avg

Used by program	Section	Type	Parameter label	Placeholder
stackops	parameter input/output	binary	Average stack	(empty)

Parameter backgr_subtr

Used by program	Section	Type	Parameter label	Placeholder
extract	parameter input/output	binary	Perform micrograph background subtraction(new picker only)	(empty)
pick	search controls	binary	Perform micrograph background subtraction(new picker only)	(empty)
pick_extract	parameter input/output	binary	Perform micrograph background subtraction(new picker only)	(empty)
reextract	parameter input/output	binary	Perform micrograph background subtraction(new picker only)	(empty)

Parameter balance

Used by program	Section	Type	Parameter label	Placeholder
selection	parameter input/output	binary	Balanced selection of particles across classes	(empty)

Parameter bandwidth_mode

Used by program	Section	Type	Parameter label	Placeholder
cls_split	filter controls	multi	Diffusion-map bandwidth mode	(empty)
denoise_project	filter controls	multi	Diffusion-map bandwidth mode	(empty)
flex_analysis	filter controls	multi	Diffusion-map bandwidth mode	(empty)
ppca_denoise	filter controls	multi	Diffusion-map bandwidth mode	(empty)

Parameter bandwidth_tune

Used by program	Section	Type	Parameter label	Placeholder
cls_split	filter controls	num	Ferguson bandwidth multiplier (default 1)	e.g. 10
denoise_project	filter controls	num	Ferguson bandwidth multiplier (default 1)	e.g. 10
flex_analysis	filter controls	num	Ferguson bandwidth multiplier (default 1)	e.g. 10
ppca_denoise	filter controls	num	Ferguson bandwidth multiplier (default 1)	e.g. 10

Parameter beamtilt

Used by program	Section	Type	Parameter label	Placeholder
assign_optics_groups	parameter input/output	binary	Use beamtilts in optics group assignment	(empty)
preproc	search controls	binary	Use beamtilts in optics group assignment	(empty)

Parameter bfac

Used by program	Section	Type	Parameter label	Placeholder
ctfops	filter controls	num	CTF B-factor	e.g. 10
filter	filter controls	num	B-factor of Gaussian low-/high-pass filter	e.g. 10
motion_correct	search controls	num	B-factor applied to frames	e.g. 10
postprocess	filter controls	num	B-factor for sharpening	e.g. 10
preproc	filter controls	num	B-factor for sharpening	e.g. 10
preprocess	search controls	num	B-factor applied to frames	e.g. 10
simulate_movie	filter controls	num	CTF B-factor	e.g. 10
simulate_particles	filter controls	num	CTF B-factor	e.g. 10
tseries_make_pickavg	search controls	num	B-factor applied to frames	e.g. 10
tseries_motion_correct	search controls	num	B-factor applied to frames	e.g. 10
volops	filter controls	num	B-factor for sharpening	e.g. 10

Parameter bfacerr

Used by program	Section	Type	Parameter label	Placeholder
simulate_particles	filter controls	num	B-factor error	e.g. 10

Parameter binwidth

Used by program	Section	Type	Parameter label	Placeholder
automask	mask controls	num	Envelope binary layers width	e.g. 10

Parameter box

Used by program	Section	Type	Parameter label	Placeholder
crys_score	parameter input/output	num	Particle box size	e.g. 10
extract	parameter input/output	num	Particle box size	e.g. 10
noisevol	parameter input/output	num	Particle box size	e.g. 10
print_dose_weights	parameter input/output	num	Particle box size	e.g. 10
print_fsc	parameter input/output	num	Particle box size	e.g. 10
print_magic_boxes	parameter input/output	num	Particle box size	e.g. 10
reextract	parameter input/output	num	Particle box size	e.g. 10
simulate_nanoparticle	parameter input/output	num	Particle box size	e.g. 10
simulate_noise	parameter input/output	num	Particle box size	e.g. 10

Parameter box_coarse

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Box size for coarse sieving	e.g. 10
sieve_cavgs	search controls	num	Coarse-pass box size	e.g. 10

Parameter box_extract

Used by program	Section	Type	Parameter label	Placeholder
master	parameter input/output	int	Force box size (px, optional)	e.g. 10
pick_extract	parameter input/output	num	Extracted particle image size	e.g. 10
tseries_extractor	parameter input/output	num	Extracted particle image size	e.g. 10

Parameter box_fine

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Box size for fine sieving	e.g. 10
sieve_cavgs	search controls	num	Fine-pass box size	e.g. 10

Parameter boxes

Used by program	Section	Type	Parameter label	Placeholder
print_project_field	parameter input/output	binary	output coordinates in JSON format	(empty)

Parameter boxfile

Used by program	Section	Type	Parameter label	Placeholder
track_particles	file input/output	file	List of particle coordinates	e.g. coords.box
tseries_motion_correct	file input/output	file	List of particle coordinates	e.g. coords.box

Parameter boxtab

Used by program	Section	Type	Parameter label	Placeholder
import_boxes	file input/output	file	List of box files	e.g. boxes.txt
import_movies	file input/output	file	List of box files	e.g. boxes.txt

Parameter cavg_ini

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	binary	3D initialization on class averages	(empty)

Parameter cavg_ini_ext

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	binary	External class-average 3D initialization	(empty)

Parameter cenlp

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	filter controls	num	Centering low-pass limit	e.g. 10
abinitio2D_chunks	filter controls	num	Centering low-pass limit	e.g. 10
abinitio3D	filter controls	num	Centering low-pass limit	e.g. 10
abinitio3D_cavgs	filter controls	num	Centering low-pass limit	e.g. 10
abinitio3D_nano	filter controls	num	Centering low-pass limit	e.g. 10
autorefine3D_nano	filter controls	num	Centering low-pass limit	e.g. 10
center	filter controls	num	Centering low-pass limit	e.g. 10
cluster2D_nano	filter controls	num	Centering low-pass limit	e.g. 10
refine3D	filter controls	num	Centering low-pass limit	e.g. 10
refine3D_nano	filter controls	num	Centering low-pass limit	e.g. 10
symaxis_search	filter controls	num	Centering low-pass limit	e.g. 10
symmetrize_map	filter controls	num	Centering low-pass limit	e.g. 10
symmetry_test	filter controls	num	Centering low-pass limit	e.g. 10
track_particles	filter controls	num	Centering low-pass limit	e.g. 10

Parameter center

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	binary	Center class averages	(empty)
abinitio2D_chunks	search controls	binary	Center class averages	(empty)
abinitio2D_stream	search controls	binary	Center class averages	(empty)
abinitio3D	search controls	binary	Center reference volume(s)	(empty)
abinitio3D_cavgs	search controls	binary	Center reference volume(s)	(empty)
autorefine3D_nano	search controls	binary	Center reference volume(s)	(empty)
center2D_nano	search controls	binary	Center class averages	(empty)
cluster2D_nano	search controls	binary	Center class averages	(empty)
mask	search controls	binary	Center input volume	(empty)
refine3D	search controls	binary	Center reference volume(s)	(empty)
refine3D_auto	search controls	binary	Center reference volume(s)	(empty)
refine3D_multi	search controls	binary	Center reference volume(s)	(empty)
refine3D_nano	search controls	binary	Center reference volume(s)	(empty)
symaxis_search	search controls	binary	Center input volume	(empty)
symmetrize_map	search controls	binary	Center input volume	(empty)
symmetry_test	search controls	binary	Center input volume	(empty)

Parameter center_pdb

Used by program	Section	Type	Parameter label	Placeholder
pdb2mrc	parameter input/output	binary	Whether to move the PDB atomic center to the center of the box	(empty)

Parameter chunk_count_penalty

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Chunk-count penalty	e.g. 10

Parameter chunk_max_len

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Maximum latent chunk length	e.g. 10

Parameter chunk_max_shift

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Maximum boundary shift	e.g. 10

Parameter chunk_min_len

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Minimum latent chunk length	e.g. 10

Parameter chunk_mode

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	multi	Trajectory chunking mode	(empty)

Parameter ciffile

Used by program	Section	Type	Parameter label	Placeholder
cif2mrc	file input/output	file	PDBx/mmCIF input coordinates file	e.g. molecule.cif
cif2pdb	file input/output	file	PDBx/mmCIF input coordinates file	e.g. molecule.cif

Parameter class

Used by program	Section	Type	Parameter label	Placeholder
cls_split	parameter input/output	num	Optional class index to split	e.g. 10
extract_subproj	parameter input/output	num	2D class index	e.g. 10
stackops	parameter input/output	num	Class index	e.g. 10

Parameter classtats

Used by program	Section	Type	Parameter label	Placeholder
oristats	parameter input/output	binary	Class statistics	(empty)

Parameter clip

Used by program	Section	Type	Parameter label	Placeholder
scale	parameter input/output	num	Clipped box size	e.g. 10
stack	parameter input/output	num	Clipped box size	e.g. 10

Parameter cls_init

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	multi	Scheme for initial class generation	(empty)

Parameter clust_crit

Used by program	Section	Type	Parameter label	Placeholder
cluster_cavgs	search controls	multi	Clustering criterion	(empty)
cluster_cavgs_selection	search controls	multi	Clustering criterion	(empty)
cluster_stack	search controls	multi	Clustering criterion	(empty)
match_cavgs	search controls	multi	Clustering criterion	(empty)
match_stacks	search controls	multi	Clustering criterion	(empty)

Parameter clustind

Used by program	Section	Type	Parameter label	Placeholder
extract_subproj	parameter input/output	num	Cluster index	e.g. 10
select_clusters	parameter input/output	num	Cluster index	e.g. 10

Parameter clustinds

Used by program	Section	Type	Parameter label	Placeholder
select_clusters	parameter input/output	str	Comma separated cluster indices	e.g. value

Parameter cn_stop

Used by program	Section	Type	Parameter label	Placeholder
symmetry_test	search controls	num	Rotational symmetry order stop index	e.g. 10

Parameter combine_eo

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_rec3D	filter controls	binary	Whether e/o references are combined for final alignment(yes|no){no}	(empty)
refine3D	filter controls	binary	Whether e/o references are combined for final alignment(yes|no){no}	(empty)
refine3D_auto	filter controls	binary	Whether e/o references are combined for final alignment(yes|no){no}	(empty)

Parameter conical_fsc

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	filter controls	binary	Conical FSC regularization	(empty)
abinitio3D_cavgs	filter controls	binary	Conical FSC regularization	(empty)
refine3D	filter controls	binary	Conical FSC regularization	(empty)

Parameter continue

Used by program	Section	Type	Parameter label	Placeholder
refine3D	search controls	binary	Continue previous refinement	(empty)
refine3D_auto	search controls	binary	Continue previous refinement	(empty)
refine3D_multi	search controls	binary	Continue previous refinement	(empty)
refine3D_nano	search controls	binary	Continue previous refinement	(empty)

Parameter cs

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	num	Spherical aberration	e.g. 10
import_movies	parameter input/output	num	Spherical aberration	e.g. 10
import_particles	parameter input/output	num	Spherical aberration	e.g. 10
master	parameter input/output	float	Spherical aberration (mm)	e.g. 10
mini_stream	parameter input/output	num	Spherical aberration	e.g. 10
preproc	parameter input/output	num	Spherical aberration	e.g. 10
simulate_movie	parameter input/output	num	Spherical aberration	e.g. 10
simulate_particles	parameter input/output	num	Spherical aberration	e.g. 10
tseries_import	parameter input/output	num	Spherical aberration	e.g. 10

Parameter ctf

Used by program	Section	Type	Parameter label	Placeholder
ctfops	filter controls	multi	CTF status	(empty)
import_movies	parameter input/output	multi	CTF status	(empty)
import_particles	parameter input/output	multi	CTF status	(empty)
oriops	parameter input/output	multi	CTF status	(empty)
reimport_particles	parameter input/output	multi	CTF status	(empty)
simulate_movie	parameter input/output	multi	CTF status	(empty)
simulate_particles	parameter input/output	multi	CTF status	(empty)

Parameter ctf_correct_mode

Used by program	Section	Type	Parameter label	Placeholder
ctf_correct	parameter input/output	multi	CTF correction mode	(empty)

Parameter ctfpatch

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	binary	Patch CTF estimation	(empty)
ctf_estimate	parameter input/output	binary	Patch CTF estimation	(empty)
mini_stream	parameter input/output	binary	Patch CTF estimation	(empty)
preproc	parameter input/output	binary	Patch CTF estimation	(empty)
preprocess	parameter input/output	binary	Patch CTF estimation	(empty)

Parameter ctfresthreshold

Used by program	Section	Type	Parameter label	Placeholder
pick_extract	filter controls	num	CTF Resolution rejection threshold	e.g. 10
preproc	filter controls	num	CTF Resolution rejection threshold	e.g. 10
selection	parameter input/output	num	CTF Resolution rejection threshold	e.g. 10

Parameter ctfstats

Used by program	Section	Type	Parameter label	Placeholder
oristats	parameter input/output	binary	CTF statistics	(empty)

Parameter defocus

Used by program	Section	Type	Parameter label	Placeholder
simulate_movie	parameter input/output	num	Underfocus	e.g. 10
simulate_particles	parameter input/output	num	Underfocus	e.g. 10

Parameter deftab

Used by program	Section	Type	Parameter label	Placeholder
ctfops	file input/output	file	CTF parameter file	e.g. deftab.txt
import_movies	file input/output	file	Pre-determined per-micrograph CTF parameters	e.g. deftab.txt
import_particles	file input/output	file	CTF parameter file	e.g. deftab.txt
import_trajectory	file input/output	file	CTF parameter file	e.g. deftab.txt
simulate_particles	file input/output	file	CTF parameter file	e.g. deftab.txt

Parameter deselfile

Used by program	Section	Type	Parameter label	Placeholder
selection	file input/output	file	File with deselection indices	e.g. deselected.txt

Parameter dferr

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	num	Underfocus error half-width	e.g. 10
simulate_particles	parameter input/output	num	Underfocus error half-width	e.g. 10

Parameter dfmax

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	num	Expected maximum defocus	e.g. 10
ctf_estimate	search controls	num	Expected maximum defocus	e.g. 10
mini_stream	search controls	num	Expected maximum defocus	e.g. 10
preproc	search controls	num	Expected maximum defocus	e.g. 10
preprocess	search controls	num	Expected maximum defocus	e.g. 10

Parameter dfmin

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	num	Expected minimum defocus	e.g. 10
ctf_estimate	search controls	num	Expected minimum defocus	e.g. 10
mini_stream	search controls	num	Expected minimum defocus	e.g. 10
preproc	search controls	num	Expected minimum defocus	e.g. 10
preprocess	search controls	num	Expected minimum defocus	e.g. 10
selection	parameter input/output	num	Expected minimum defocus	e.g. 10

Parameter dfunit

Used by program	Section	Type	Parameter label	Placeholder
import_particles	parameter input/output	multi	Underfocus unit	(empty)

Parameter dir

Used by program	Section	Type	Parameter label	Placeholder
new_project	file input/output	dir	Project directory	e.g. project/
pick	file input/output	dir	Output directory	e.g. pick/

Parameter dir_box

Used by program	Section	Type	Parameter label	Placeholder
extract	file input/output	dir	Box files directory	e.g. boxes/

Parameter dir_exec

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D_stream	file input/output	file	Previous run directory	e.g. 3_abinitio2D_stream
pick_extract	file input/output	file	Previous run directory	e.g. 2_pick_extract
sieve_cavgs	file input/output	file	Previous run directory	e.g. 3_sieve_cavgs

Parameter dir_meta

Used by program	Section	Type	Parameter label	Placeholder
master	file input/output	dir	Input metadata directory	e.g. /path/to/folder
preproc	file input/output	dir	Directory containing per-movie metadata in XML format	e.g. /dataset/metadata

Parameter dir_movies

Used by program	Section	Type	Parameter label	Placeholder
import_movies	file input/output	dir	Input movies directory	e.g. /cryodata/
master	file input/output	dir	Input movies directory	e.g. /path/to/folder
preproc	file input/output	dir	Input movies directory	e.g. /cryodata/

Parameter dir_preprocess

Used by program	Section	Type	Parameter label	Placeholder
master	file input/output	hidden_dir	Pre-existing preprocessing directory	(empty)

Parameter dir_prev

Used by program	Section	Type	Parameter label	Placeholder
preproc	file input/output	file	Previous run directory	e.g. 2_preproc

Parameter dir_target

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D_stream	file input/output	file	Target directory	e.g. 2_pick_extract
assign_optics	file input/output	file	Target directory	e.g. 1_preproc
gen_pickrefs	file input/output	file	Target directory	e.g. 1_preproc
pick_extract	file input/output	file	Target directory	e.g. 1_preproc
sieve_cavgs	file input/output	file	Target directory	e.g. 2_pick_extract

Parameter dm_alpha

Used by program	Section	Type	Parameter label	Placeholder
cls_split	filter controls	num	Diffusion-map density normalization (default 0)	e.g. 10
denoise_project	filter controls	num	Diffusion-map density normalization (default 0)	e.g. 10
ppca_denoise	filter controls	num	Diffusion-map density normalization (default 0)	e.g. 10

Parameter e1

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	num	Rotation along Phi	e.g. 10
volops	parameter input/output	num	Rotation along Phi	e.g. 10

Parameter e2

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	num	Rotation along Theta	e.g. 10
volops	parameter input/output	num	Rotation along Theta	e.g. 10

Parameter e3

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	num	Rotation along Psi	e.g. 10
volops	parameter input/output	num	Rotation along Psi	e.g. 10

Parameter edge

Used by program	Section	Type	Parameter label	Placeholder
automask	mask controls	num	Envelope mask soft edge	e.g. 10
automask2D	mask controls	num	Envelope mask soft edge	e.g. 10
gen_pickrefs	mask controls	num	Automask soft edge	e.g. 10
mask	mask controls	num	Envelope mask soft edge	e.g. 10

Parameter eer_fraction

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	parameter input/output	num	# of EER frames to fraction together	e.g. 10
preproc	parameter input/output	num	# of EER frames to fraction together	e.g. 10
preprocess	parameter input/output	num	# of EER frames to fraction together	e.g. 10

Parameter element

Used by program	Section	Type	Parameter label	Placeholder
analysis2D_nano	parameter input/output	str	Atom element name: Au, Pt etc.	e.g. value
atoms_rmsd	filter controls	str	Atom element name: Au, Pt etc.	e.g. value
atoms_stats	filter controls	str	Atom element name: Au, Pt etc.	e.g. value
autorefine3D_nano	parameter input/output	str	Atom element name: Au, Pt etc.	e.g. value
conv_atom_denoise	filter controls	str	Atom element name: Au, Pt etc.	e.g. value
core_atoms_analysis	filter controls	str	Atom element name: Au, Pt etc.	e.g. value
crys_score	filter controls	str	Atom element name: Au, Pt etc.	e.g. value
detect_atoms	filter controls	str	Atom element name: Au, Pt etc.	e.g. value
simulate_nanoparticle	parameter input/output	str	Atom element name: Au, Pt etc.	e.g. value

Parameter envfsc

Used by program	Section	Type	Parameter label	Placeholder
reconstruct3D	filter controls	binary	Envelope mask e/o maps for FSC	(empty)
refine3D	filter controls	binary	Envelope mask e/o maps for FSC	(empty)

Parameter eo_stage

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	binary	Use even/odd stage	(empty)

Parameter even

Used by program	Section	Type	Parameter label	Placeholder
make_oris	parameter input/output	binary	Generate even projections	(empty)
simulate_particles	parameter input/output	binary	Generate even projections	(empty)

Parameter extr_lim

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	num	Extreme-particle iteration limit	e.g. 10

Parameter fbody

Used by program	Section	Type	Parameter label	Placeholder
fsc_area_score	parameter input/output	string	Output file body	e.g. value
motion_correct	parameter input/output	string	Template output micrograph name	e.g. value
preprocess	parameter input/output	string	Template output micrograph name	e.g. value
track_particles	parameter input/output	string	Template output tracked series	e.g. value
tseries_extractor	parameter input/output	string	Output file body	e.g. value

Parameter filetab

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	file input/output	file	List of files	e.g. input_files.txt
import_movies	file input/output	file	List of movie files	e.g. input_files.txt
mini_stream	file input/output	file	List of files	e.g. input_files.txt
model_cavgs_rejection	file input/output	file	Analysis file table	e.g. input_files.txt
scale	file input/output	file	Stacks list	e.g. input_files.txt
stack	file input/output	file	Stacks list	e.g. input_files.txt
tsegmaps_core_finder	file input/output	file	Volumes list	e.g. input_files.txt
tseries_import	file input/output	file	List of individual movie frame files	e.g. input_files.txt
volanalyze	file input/output	file	Volumes list	e.g. input_files.txt
volcluster	file input/output	file	Volumes list	e.g. input_files.txt

Parameter fill_holes

Used by program	Section	Type	Parameter label	Placeholder
binarize	parameter input/output	binary	Fill holes	(empty)

Parameter filt_mode

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	filter controls	multi	Filtering mode	(empty)
refine3D_auto	filter controls	multi	Filtering mode	(empty)
refine3D_multi	filter controls	multi	Filtering mode	(empty)

Parameter filter

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	multi	Filter type(bs|nlmean|no){no}	(empty)
track_particles	filter controls	multi	Alternative filter for particle tracking	(empty)

Parameter fit_phshift

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	binary	Fit CTF phase shift	(empty)
ctf_estimate	parameter input/output	binary	Fit CTF phase shift	(empty)
master	parameter input/output	binary	Phase plate	(empty)
mini_stream	parameter input/output	binary	Fit CTF phase shift	(empty)
preproc	parameter input/output	binary	Fit CTF phase shift	(empty)
preprocess	parameter input/output	binary	Fit CTF phase shift	(empty)

Parameter flipgain

Used by program	Section	Type	Parameter label	Placeholder
fractionate_movies	parameter input/output	multi	Flip the gain reference	(empty)
master	image input/output	multi	Gain processing	(empty)
motion_correct	parameter input/output	multi	Flip the gain reference	(empty)
preproc	parameter input/output	multi	Flip the gain reference	(empty)
preprocess	parameter input/output	multi	Flip the gain reference	(empty)

Parameter fname

Used by program	Section	Type	Parameter label	Placeholder
atoms_register	file input/output	file	PDB file list	e.g. pdb_files.txt
crys_score	file input/output	file	PDB file list	e.g. np_pdbs.txt
info_image	file input/output	file	Name of image file	e.g. image.mrc
model_cavgs_rejection	file input/output	file	Quality model output	e.g. cavgs_quality_output.txt
write_mic_filetab	file input/output	file	Filename micrograph list	e.g. mics.txt

Parameter force_lp_range

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	filter controls	binary	Force low-pass range	(empty)

Parameter frac_best

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_cavgs	parameter input/output	num	Anchor fraction	e.g. 10
sample_classes	parameter input/output	num	Fraction of best particles to sample from	e.g. 10

Parameter frac_diam

Used by program	Section	Type	Parameter label	Placeholder
atoms_rmsd	parameter input/output	num	Fraction of atomic diameter	e.g. 10
core_atoms_analysis	parameter input/output	num	Fraction of atomic diameter	e.g. 10

Parameter frac_worst

Used by program	Section	Type	Parameter label	Placeholder
sample_classes	parameter input/output	num	Fraction of worst particles to sample from	e.g. 10

Parameter fraca

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	num	Amplitude contrast fraction	e.g. 10
import_movies	parameter input/output	num	Amplitude contrast fraction	e.g. 10
import_particles	parameter input/output	num	Amplitude contrast fraction	e.g. 10
master	parameter input/output	float	Amplitude contrast fraction	e.g. 10
mini_stream	parameter input/output	num	Amplitude contrast fraction	e.g. 10
preproc	parameter input/output	num	Amplitude contrast fraction	e.g. 10
simulate_movie	parameter input/output	num	Amplitude contrast fraction	e.g. 10
simulate_particles	parameter input/output	num	Amplitude contrast fraction	e.g. 10
tseries_import	parameter input/output	num	Amplitude contrast fraction	e.g. 10

Parameter fraction_dose_target

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	parameter input/output	num	EER fraction dose target (e/Ang^2)	e.g. 10
preproc	parameter input/output	num	EER fraction dose target (e/Ang^2)	e.g. 10
preprocess	parameter input/output	num	EER fraction dose target (e/Ang^2)	e.g. 10

Parameter frcs

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	str	Projection FRCs file	e.g. value
print_fsc	parameter input/output	str	Projection FRCs file	e.g. value

Parameter fromf

Used by program	Section	Type	Parameter label	Placeholder
fractionate_movies	parameter input/output	num	Starting frame	e.g. 10
track_particles	parameter input/output	num	Frame to start tracking from	e.g. 10
tseries_make_pickavg	parameter input/output	num	Frame to start averaging from	e.g. 10

Parameter fromp

Used by program	Section	Type	Parameter label	Placeholder
extract_subproj	parameter input/output	num	From index	e.g. 10
extract_substk	parameter input/output	num	From index	e.g. 10
scale	parameter input/output	num	First stack index	e.g. 10
stackops	parameter input/output	num	From particle index	e.g. 10
trajectory_reconstruct3D	parameter input/output	num	From particle index	e.g. 10

Parameter fsc

Used by program	Section	Type	Parameter label	Placeholder
ctf_correct	filter controls	file	FSC file	e.g. fsc.bin
filter	filter controls	file	FSC file	e.g. fsc.bin
postprocess	filter controls	file	FSC file	e.g. fsc.bin
print_fsc	file input/output	file	FSC file	e.g. fsc.bin

Parameter gainref

Used by program	Section	Type	Parameter label	Placeholder
master	file input/output	file	Gain reference	e.g. gainref.mrc
motion_correct	file input/output	file	Gain reference	e.g. gainref.mrc
preproc	file input/output	file	Gain reference	e.g. gainref.mrc
preprocess	file input/output	file	Gain reference	e.g. gainref.mrc

Parameter graph

Used by program	Section	Type	Parameter label	Placeholder
cls_split	filter controls	multi	Class split graph	(empty)
denoise_project	filter controls	multi	Diffusion graph	(empty)

Parameter greedy_sampling

Used by program	Section	Type	Parameter label	Placeholder
sample_classes	parameter input/output	binary	Greedy balanced selection	(empty)
selection	parameter input/output	binary	Greedy balanced selection	(empty)

Parameter guinier

Used by program	Section	Type	Parameter label	Placeholder
volops	parameter input/output	binary	Guinier plot	(empty)

Parameter hp

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	filter controls	num	High-pass limit	e.g. 10
abinitio2D_chunks	filter controls	num	High-pass limit	e.g. 10
abinitio3D	filter controls	num	High-pass limit	e.g. 10
abinitio3D_cavgs	filter controls	num	High-pass limit	e.g. 10
abinitio3D_nano	filter controls	num	High-pass limit	e.g. 10
autorefine3D_nano	filter controls	num	High-pass limit	e.g. 10
check_refpick	filter controls	num	High-pass limit	e.g. 10
cluster2D_nano	filter controls	num	High-pass limit	e.g. 10
cluster_cavgs	filter controls	num	High-pass limit	e.g. 10
cluster_cavgs_selection	filter controls	num	High-pass limit	e.g. 10
cluster_stack	filter controls	num	High-pass limit	e.g. 10
ctf_estimate	filter controls	num	High-pass limit	e.g. 10
dock_volpair	filter controls	num	High-pass limit	e.g. 10
filter	filter controls	num	High-pass limit	e.g. 10
fsc	filter controls	num	High-pass limit	e.g. 10
match_cavgs	filter controls	num	High-pass limit	e.g. 10
match_stacks	filter controls	num	High-pass limit	e.g. 10
mini_stream	filter controls	num	High-pass limit	e.g. 10
ppca_denoise	filter controls	num	High-pass limit	e.g. 10
refine3D	filter controls	num	High-pass limit	e.g. 10
refine3D_nano	filter controls	num	High-pass limit	e.g. 10
symaxis_search	filter controls	num	High-pass limit	e.g. 10
symmetrize_map	filter controls	num	High-pass limit	e.g. 10
symmetry_test	filter controls	num	High-pass limit	e.g. 10
track_particles	filter controls	num	High-pass limit	e.g. 10
trajectory_denoise	filter controls	num	High-pass limit	e.g. 10
volanalyze	filter controls	num	High-pass limit	e.g. 10
volcluster	filter controls	num	High-pass limit	e.g. 10
volops	filter controls	num	High-pass limit	e.g. 10

Parameter hp_ctf_estimate

Used by program	Section	Type	Parameter label	Placeholder
preproc	filter controls	num	CTF estimation high-pass limit	e.g. 10
preprocess	filter controls	num	High-pass limit for CTF parameter estimation	e.g. 10

Parameter icefracthreshold

Used by program	Section	Type	Parameter label	Placeholder
pick_extract	filter controls	num	Ice Fraction rejection threshold	e.g. 10
selection	parameter input/output	num	Ice Fraction rejection threshold	e.g. 10

Parameter icm

Used by program	Section	Type	Parameter label	Placeholder
autorefine3D_nano	filter controls	binary	Whether to perform ICM filtering of reference(s)	(empty)
flex_analysis	filter controls	binary	Automatic diffusion-mode selection	(empty)
refine3D_nano	filter controls	binary	Whether to perform ICM filtering of reference(s)	(empty)
uniform_filter3D	filter controls	binary	Whether to perform ICM filtering of reference(s)	(empty)

Parameter imgkind

Used by program	Section	Type	Parameter label	Placeholder
postprocess	parameter input/output	str	Volume kind	e.g. value

Parameter import_dir

Used by program	Section	Type	Parameter label	Placeholder
import_starproject	file input/output	dir	Import directory	e.g. MotionCorr/job001

Parameter import_type

Used by program	Section	Type	Parameter label	Placeholder
import_starproject	parameter input/output	multi	Import type	(empty)

Parameter infile

Used by program	Section	Type	Parameter label	Placeholder
model_cavgs_rejection	file input/output	file	Quality model input	e.g. cavgs_quality_model.txt
selection	file input/output	file	File with selection state (0/1) flags	e.g. selection.txt
tseries_extractor	file input/output	file	Selected particle trajectory	e.g. trajectory.txt

Parameter job_memory_per_task

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	str	Memory per computing node	e.g. value
update_project	computer controls	str	Memory per computing node	e.g. value

Parameter json

Used by program	Section	Type	Parameter label	Placeholder
print_project_field	parameter input/output	binary	output in JSON format	(empty)

Parameter k_nn

Used by program	Section	Type	Parameter label	Placeholder
cls_split	parameter input/output	num	Diffusion graph neighbors (default 10; try 5-30)	e.g. 10
denoise_project	filter controls	num	Diffusion graph neighbors (default 10; try 5-30)	e.g. 10
flex_analysis	filter controls	num	Nearest neighbors (default 100)	e.g. 10
ppca_denoise	filter controls	num	Diffusion graph neighbors (default 5; try 5-30)	e.g. 10
trajectory_denoise	filter controls	num	Diffusion graph neighbors (default 5; try 5-30)	e.g. 10
trajectory_reconstruct3D	search controls	num	Nearest neighbors	e.g. 10

Parameter kpca_backend

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise	filter controls	multi	Kernel PCA backend	(empty)
ppca_denoise_classes	filter controls	multi	Kernel PCA backend	(empty)
trajectory_denoise	filter controls	multi	Kernel PCA backend	(empty)

Parameter kpca_ker

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise	filter controls	multi	Kernel PCA kernel	(empty)
ppca_denoise_classes	filter controls	multi	Kernel PCA kernel	(empty)
trajectory_denoise	filter controls	multi	Kernel PCA kernel	(empty)

Parameter kpca_nystrom_local_nbrs

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise	filter controls	num	Nyström max local support neighbors (default 96; try 96, 128)	e.g. 10
ppca_denoise_classes	filter controls	num	Nyström max local support neighbors (default 96; try 96, 128)	e.g. 10
trajectory_denoise	filter controls	num	Nyström max local support neighbors (default 96; try 96, 128)	e.g. 10

Parameter kpca_nystrom_npts

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise	filter controls	num	Nyström landmark count (0 => auto=max(128,2*neigs), capped at 512; try 256, 512)	e.g. 10
ppca_denoise_classes	filter controls	num	Nyström landmark count (0 => auto=max(128,2*neigs), capped at 512; try 256, 512)	e.g. 10
trajectory_denoise	filter controls	num	Nyström landmark count (0 => auto=max(128,2*neigs), capped at 512; try 256, 512)	e.g. 10

Parameter kpca_rbf_gamma

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise	filter controls	num	RBF gamma (0 => auto)	e.g. 10
ppca_denoise_classes	filter controls	num	RBF gamma (0 => auto)	e.g. 10
trajectory_denoise	filter controls	num	RBF gamma (0 => auto)	e.g. 10

Parameter kv

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	num	Acceleration voltage	e.g. 10
import_movies	parameter input/output	num	Acceleration voltage	e.g. 10
import_particles	parameter input/output	num	Acceleration voltage	e.g. 10
master	parameter input/output	int	Acceleration voltage (kV)	e.g. 10
mini_stream	parameter input/output	num	Acceleration voltage	e.g. 10
preproc	parameter input/output	num	Acceleration voltage	e.g. 10
print_dose_weights	parameter input/output	num	Acceleration voltage	e.g. 10
simulate_movie	parameter input/output	num	Acceleration voltage	e.g. 10
simulate_particles	parameter input/output	num	Acceleration voltage	e.g. 10
tseries_import	parameter input/output	num	Acceleration voltage	e.g. 10

Parameter lambda

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	num	BS smoother lambda	e.g. 10
icm2D	filter controls	num	ICM lambda regularization parameter	e.g. 10
icm3D	filter controls	num	ICM lambda regularization parameter	e.g. 10
refine3D_nano	filter controls	num	ICM lambda regularization parameter	e.g. 10
uniform_filter3D	filter controls	num	ICM lambda regularization parameter	e.g. 10

Parameter lp

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	filter controls	num	Low-pass limit	e.g. 10
abinitio2D_chunks	filter controls	num	Low-pass limit	e.g. 10
abinitio3D	filter controls	num	Low-pass limit	e.g. 10
autorefine3D_nano	filter controls	num	Initial low-pass limit	e.g. 10
check_refpick	filter controls	num	Low-pass limit	e.g. 10
cluster2D_nano	filter controls	num	Static low-pass limit	e.g. 10
cluster_cavgs	filter controls	num	Low-pass limit	e.g. 10
cluster_cavgs_selection	filter controls	num	Low-pass limit	e.g. 10
cluster_stack	filter controls	num	Low-pass limit	e.g. 10
ctf_estimate	filter controls	num	Low-pass limit	e.g. 10
dock_volpair	filter controls	num	Low-pass limit	e.g. 10
estimate_diam	filter controls	num	low-pass limit in Angstroms{7.}	e.g. 10
filter	filter controls	num	Low-pass limit	e.g. 10
flex_analysis	filter controls	num	Low-pass limit	e.g. 10
fsc	filter controls	num	Low-pass limit	e.g. 10
match_cavgs	filter controls	num	Low-pass limit	e.g. 10
match_stacks	filter controls	num	Low-pass limit	e.g. 10
mini_stream	filter controls	num	Low-pass limit	e.g. 10
pick	filter controls	num	Low-pass limit	e.g. 10
postprocess	filter controls	num	Low-pass limit for map filtering	e.g. 10
ppca_denoise	filter controls	num	Low-pass limit	e.g. 10
refine3D	filter controls	num	Static low-pass limit	e.g. 10
refine3D_nano	filter controls	num	Static low-pass limit	e.g. 10
symaxis_search	filter controls	num	Low-pass limit	e.g. 10
symmetrize_map	filter controls	num	Low-pass limit	e.g. 10
symmetry_test	filter controls	num	Low-pass limit	e.g. 10
track_particles	filter controls	num	Low-pass limit in Angs	e.g. 10
trajectory_denoise	filter controls	num	Low-pass limit	e.g. 10
trajectory_reconstruct3D	filter controls	num	Low-pass limit	e.g. 10
volanalyze	filter controls	num	Low-pass limit	e.g. 10
volcluster	filter controls	num	Low-pass limit	e.g. 10
volops	filter controls	num	Low-pass limit	e.g. 10

Parameter lp_backgr

Used by program	Section	Type	Parameter label	Placeholder
mask	filter controls	num	Background low-pass resolution	e.g. 10
refine3D	filter controls	num	Background low-pass resolution	e.g. 10

Parameter lp_ctf_estimate

Used by program	Section	Type	Parameter label	Placeholder
preproc	filter controls	num	CTF estimation low-pass limit	e.g. 10
preprocess	filter controls	num	Low-pass limit for CTF parameter estimation	e.g. 10

Parameter lp_pick

Used by program	Section	Type	Parameter label	Placeholder
pick_extract	filter controls	num	Low-pass limit for picking	e.g. 10

Parameter lplim_crit

Used by program	Section	Type	Parameter label	Placeholder
fsc_area_score	filter controls	num	Low-pass limit FSC criterion	e.g. 10
refine3D	filter controls	num	Low-pass limit FSC criterion	e.g. 10

Parameter lpstart

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	filter controls	num	Initial low-pass limit	e.g. 10
abinitio3D	filter controls	num	Starting low-pass limit	e.g. 10
abinitio3D_cavgs	filter controls	num	Starting low-pass limit	e.g. 10
abinitio3D_nano	filter controls	num	Starting low-pass limit	e.g. 10
cluster2D_nano	filter controls	num	Initial low-pass limit	e.g. 10
motion_correct	filter controls	num	Initial low-pass limit	e.g. 10
particle_sieving	filter controls	num	Initial low-pass limit	e.g. 10
preproc	filter controls	num	Motion-correction low-pass start	e.g. 10
preprocess	filter controls	num	Initial low-pass limit for movie alignment	e.g. 10
sieve_cavgs	filter controls	num	Initial sieving low-pass limit	e.g. 10
tseries_make_pickavg	filter controls	num	Initial low-pass limit	e.g. 10
tseries_motion_correct	filter controls	num	Initial low-pass limit	e.g. 10
uniform_filter2D	filter controls	num	Starting resolution limit	e.g. 10
uniform_filter3D	filter controls	num	Starting resolution limit	e.g. 10

Parameter lpstart_ini3D

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	filter controls	num	Starting low-pass limit ini3D	e.g. 10

Parameter lpstop

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	filter controls	num	Final low-pass limit	e.g. 10
abinitio2D_chunks	filter controls	num	Final low-pass limit	e.g. 10
abinitio3D	filter controls	num	Final low-pass limit	e.g. 10
abinitio3D_cavgs	filter controls	num	Final low-pass limit	e.g. 10
abinitio3D_nano	filter controls	num	Final low-pass limit	e.g. 10
cluster2D_nano	filter controls	num	Final low-pass limit	e.g. 10
motion_correct	filter controls	num	Final low-pass limit	e.g. 10
preproc	filter controls	num	Motion-correction low-pass stop	e.g. 10
preprocess	filter controls	num	Final low-pass limit for movie alignment	e.g. 10
refine3D	filter controls	num	Low-pass limit for frequency limited refinement	e.g. 10
refine3D_multi	filter controls	num	Low-pass limit for frequency limited refinement	e.g. 10
refine3D_nano	filter controls	num	Low-pass limit for frequency limited refinement	e.g. 10
tseries_make_pickavg	filter controls	num	Final low-pass limit	e.g. 10
tseries_motion_correct	filter controls	num	Final low-pass limit	e.g. 10
uniform_filter2D	filter controls	num	Stopping resolution limit	e.g. 10
uniform_filter3D	filter controls	num	Stopping resolution limit	e.g. 10

Parameter lpstop_coarse

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	filter controls	num	Final low-pass limit for coarse sieving	e.g. 10
sieve_cavgs	filter controls	num	Coarse-pass low-pass limit	e.g. 10

Parameter lpstop_fine

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	filter controls	num	Final low-pass limit for fine sieving	e.g. 10
sieve_cavgs	filter controls	num	Fine-pass low-pass limit	e.g. 10

Parameter lpstop_ini3D

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	filter controls	num	Final low-pass limit ini3D	e.g. 10

Parameter makemovie

Used by program	Section	Type	Parameter label	Placeholder
stackops	parameter input/output	binary	Whether to make a movie	(empty)

Parameter max_dose

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	parameter input/output	num	Maximum dose threshold(e/A2)	e.g. 10
preproc	parameter input/output	num	Maximum dose threshold(e/A2)	e.g. 10
preprocess	parameter input/output	num	Maximum dose threshold(e/A2)	e.g. 10

Parameter maxits

Used by program	Section	Type	Parameter label	Placeholder
autorefine3D_nano	search controls	num	Max iterations	e.g. 10
cluster2D_nano	search controls	num	Max iterations	e.g. 10
reconstruct3D_pcg	filter controls	num	Max iterations	e.g. 10
refine3D	search controls	num	Max iterations	e.g. 10
refine3D_auto	search controls	num	Max iterations	e.g. 10
refine3D_multi	search controls	num	Max iterations	e.g. 10
refine3D_nano	search controls	num	Max iterations	e.g. 10
trajectory_reconstruct3D	search controls	num	Max iterations	e.g. 10

Parameter maxnchunks

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Max # of chunks to process	e.g. 10
sieve_cavgs	search controls	num	Number of subsets after which 2D analysis ends	e.g. 10

Parameter maxpop

Used by program	Section	Type	Parameter label	Placeholder
assign_optics_groups	parameter input/output	num	Maximum number of movies/micrographs/stacks in each optics group	e.g. 10

Parameter mcconvention

Used by program	Section	Type	Parameter label	Placeholder
fractionate_movies	parameter input/output	str	Movie alignment convention	e.g. value
motion_correct	search controls	str	Frame of reference during movie alignment	e.g. value
preproc	parameter input/output	str	Frame of reference during movie alignment	e.g. value
preprocess	search controls	str	Frame of reference during movie alignment	e.g. value

Parameter mcpatch

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	search controls	binary	Patch-based motion correction	(empty)
preproc	parameter input/output	binary	Patch-based motion correction	(empty)
preprocess	search controls	binary	Patch-based motion correction	(empty)
tseries_make_pickavg	search controls	binary	Patch-based motion correction	(empty)
tseries_motion_correct	search controls	binary	Patch-based motion correction	(empty)

Parameter mcpatch_thres

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	search controls	binary	Use motion correction patch threshold	(empty)
preproc	parameter input/output	binary	Use motion correction patch threshold	(empty)
preprocess	search controls	binary	Use motion correction patch threshold	(empty)

Parameter minits

Used by program	Section	Type	Parameter label	Placeholder
refine3D_auto	search controls	num	Minimum automatic iterations	e.g. 10

Parameter mirr

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	multi	Mirror orientations	(empty)
postprocess	filter controls	multi	Perform mirroring	(empty)
stackops	parameter input/output	multi	Perform mirroring	(empty)
volops	parameter input/output	multi	Perform mirroring	(empty)

Parameter ml_reg

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	filter controls	binary	ML regularization	(empty)
refine3D	filter controls	binary	ML regularization	(empty)
refine3D_multi	filter controls	binary	ML regularization	(empty)

Parameter moldiam

Used by program	Section	Type	Parameter label	Placeholder
cluster2D_nano	parameter input/output	num	Molecular diameter	e.g. 10
pick	parameter input/output	num	Molecular diameter	e.g. 10
pick_extract	parameter input/output	num	Molecular diameter	e.g. 10
print_magic_boxes	parameter input/output	num	Molecular diameter	e.g. 10
simulate_nanoparticle	parameter input/output	num	Molecular diameter	e.g. 10

Parameter moldiam_max

Used by program	Section	Type	Parameter label	Placeholder
mini_stream	parameter input/output	num	Max molecular diameter	e.g. 10
pick	parameter input/output	num	Max molecular diameter	e.g. 10
pick_extract	parameter input/output	num	Max molecular diameter	e.g. 10

Parameter mskdiam

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	mask controls	num	Mask diameter	e.g. 10
abinitio2D_chunks	mask controls	num	Mask diameter	e.g. 10
abinitio2D_stream	mask controls	num	Mask diameter	e.g. 10
abinitio3D	mask controls	num	Mask diameter	e.g. 10
abinitio3D_cavgs	mask controls	num	Mask diameter	e.g. 10
abinitio3D_nano	mask controls	num	Mask diameter	e.g. 10
automask2D	mask controls	num	Mask diameter	e.g. 10
autorefine3D_nano	mask controls	num	Mask diameter	e.g. 10
bootstrap_rec3D	mask controls	num	Mask diameter	e.g. 10
cavgseoproc_nano	mask controls	num	Mask diameter	e.g. 10
cavgsproc_nano	mask controls	num	Mask diameter	e.g. 10
cls_split	mask controls	num	Mask diameter	e.g. 10
cluster2D_nano	mask controls	num	Mask diameter	e.g. 10
cluster_cavgs	mask controls	num	Mask diameter	e.g. 10
cluster_cavgs_selection	mask controls	num	Mask diameter	e.g. 10
cluster_stack	mask controls	num	Mask diameter	e.g. 10
conv_atom_denoise	mask controls	num	Mask diameter	e.g. 10
denoise_project	mask controls	num	Mask diameter	e.g. 10
detect_atoms	mask controls	num	Mask diameter	e.g. 10
dock_volpair	mask controls	num	Mask diameter	e.g. 10
estimate_diam	mask controls	num	Mask diameter	e.g. 10
flex_analysis	mask controls	num	Mask diameter	e.g. 10
fsc	mask controls	num	Mask diameter	e.g. 10
fsc_area_score	mask controls	num	Mask diameter	e.g. 10
mask	mask controls	num	Mask diameter	e.g. 10
match_cavgs	mask controls	num	Mask diameter	e.g. 10
match_stacks	mask controls	num	Mask diameter	e.g. 10
model_cavgs_rejection	mask controls	num	Mask diameter	e.g. 10
normalize	mask controls	num	Mask diameter	e.g. 10
nu_filt3D	mask controls	num	Mask diameter	e.g. 10
postprocess	mask controls	num	Mask diameter	e.g. 10
ppca_denoise	mask controls	num	Mask diameter	e.g. 10
ppca_volvar	mask controls	num	Mask diameter	e.g. 10
ptclsproc_nano	mask controls	num	Mask diameter	e.g. 10
reconstruct3D	mask controls	num	Mask diameter	e.g. 10
reconstruct3D_pcg	mask controls	num	Mask diameter	e.g. 10
refine3D	mask controls	num	Mask diameter	e.g. 10
refine3D_auto	mask controls	num	Mask diameter	e.g. 10
refine3D_multi	mask controls	num	Mask diameter	e.g. 10
refine3D_nano	mask controls	num	Mask diameter	e.g. 10
reproject	mask controls	num	Mask diameter	e.g. 10
sieve_cavgs	mask controls	num	Mask diameter	e.g. 10
simulate_particles	mask controls	num	Mask diameter	e.g. 10
symaxis_search	mask controls	num	Mask diameter	e.g. 10
symmetrize_map	mask controls	num	Mask diameter	e.g. 10
symmetry_test	mask controls	num	Mask diameter	e.g. 10
trajectory_denoise	mask controls	num	Mask diameter	e.g. 10
trajectory_make_projavgs	mask controls	num	Mask diameter	e.g. 10
trajectory_reconstruct3D	mask controls	num	Mask diameter	e.g. 10
uniform_filter2D	mask controls	num	Mask diameter	e.g. 10
uniform_filter3D	mask controls	num	Mask diameter	e.g. 10
validate_cavgs_vs_model	mask controls	num	Mask diameter	e.g. 10
volanalyze	mask controls	num	Mask diameter	e.g. 10
volcluster	mask controls	num	Mask diameter	e.g. 10
volops	mask controls	num	Mask diameter	e.g. 10

Parameter mskdiam_detect

Used by program	Section	Type	Parameter label	Placeholder
autorefine3D_nano	mask controls	num	Detect-atoms mask diameter	e.g. 10

Parameter mul

Used by program	Section	Type	Parameter label	Placeholder
make_cavgs	parameter input/output	num	Shift multiplication factor	e.g. 10
oriops	parameter input/output	num	Shift multiplication factor	e.g. 10
volops	parameter input/output	num	Multiplication factor	e.g. 10

Parameter multi_moldiams

Used by program	Section	Type	Parameter label	Placeholder
pick	parameter input/output	str	Comma-separated molecular diameters with which to execute multiple gaussian pick	e.g. value

Parameter multivol_mode

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	multi	Multi-volume ab initio mode	(empty)
abinitio3D_cavgs	search controls	multi	Multi-volume class-average ab initio mode	(empty)
refine3D_multi	search controls	multi	Multi-volume refinement mode	(empty)

Parameter nang_nbrs

Used by program	Section	Type	Parameter label	Placeholder
flex_analysis	filter controls	num	Angular candidate cap (default 1000)	e.g. 10
trajectory_reconstruct3D	search controls	num	Angular candidate cap	e.g. 10

Parameter nboxes_max

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	num	Max # boxes per micrograph	e.g. 10
pick	search controls	num	Max # boxes per micrograph	e.g. 10

Parameter nchunks

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D_chunks	parameter input/output	num	Number of chunks	e.g. 10
particle_sieving	computer controls	num	Legacy concurrent-chunk alias	e.g. 10
sieve_cavgs	computer controls	num	Number of subsets to classify simultaneously	e.g. 10
trajectory_reconstruct3D	parameter input/output	num	Number of temporal chunks	e.g. 10

Parameter nchunks_max

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Maximum automatic chunk count	e.g. 10

Parameter nchunks_min

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Minimum automatic chunk count	e.g. 10

Parameter nchunksperset

Used by program	Section	Type	Parameter label	Placeholder
sieve_cavgs	search controls	num	Number of subsets to group	e.g. 10

Parameter ncls

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	num	Number of 2D clusters	e.g. 10
abinitio2D_stream	search controls	num	Maximum number of 2D clusters	e.g. 10
center2D_nano	search controls	num	Number of 2D clusters	e.g. 10
cls_split	parameter input/output	num	Fixed number of subclasses (0 => auto)	e.g. 10
cluster_cavgs	parameter input/output	num	Number of clusters	e.g. 10
cluster_stack	parameter input/output	num	Number of clusters	e.g. 10
make_cavgs	parameter input/output	num	Number of 2D clusters	e.g. 10
make_oris	parameter input/output	num	Number of random class labels	e.g. 10
pick	search controls	num	Cluster input pickrefs before template generation	e.g. 10
sieve_cavgs	search controls	num	Number of 2D clusters	e.g. 10
volcluster	parameter input/output	num	Number of 2D clusters	e.g. 10

Parameter ncls_coarse

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Number of clusters for coarse sieving	e.g. 10
sieve_cavgs	search controls	num	Coarse-pass class count	e.g. 10

Parameter ncls_fine

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Number of clusters for fine sieving	e.g. 10
sieve_cavgs	search controls	num	Fine-pass class count	e.g. 10

Parameter ncunits

Used by program	Section	Type	Parameter label	Placeholder
track_particles	computer controls	num	Concurrent particle trackers	e.g. 10

Parameter ndev

Used by program	Section	Type	Parameter label	Placeholder
binarize	parameter input/output	num	Binarization threshold	e.g. 10
pick	search controls	num	# of sigmas for outlier detection	e.g. 10

Parameter ndiscrete

Used by program	Section	Type	Parameter label	Placeholder
make_oris	parameter input/output	num	Number of discrete projection directions	e.g. 10
oriops	parameter input/output	num	Number of discrete projection directions	e.g. 10

Parameter neg

Used by program	Section	Type	Parameter label	Placeholder
ctfops	parameter input/output	binary	Invert contrast	(empty)
reproject	parameter input/output	binary	Invert contrast	(empty)
stackops	parameter input/output	binary	Invert contrast	(empty)
track_particles	parameter input/output	binary	Invert contrast	(empty)
tseries_extractor	parameter input/output	binary	Invert contrast	(empty)
volops	parameter input/output	binary	Invert contrast	(empty)

Parameter neigs

Used by program	Section	Type	Parameter label	Placeholder
cls_split	filter controls	num	Number of eigencomponents (0 => auto scan; default 200)	e.g. 10
denoise_project	filter controls	num	Number of eigencomponents (0 => auto scan; default 200)	e.g. 10
flex_analysis	filter controls	num	Maximum number of diffusion modes (default 15)	e.g. 10
ppca_denoise	filter controls	num	Number of eigencomponents (0 => auto for Nyström kPCA; default 160; try 128, 160)	e.g. 10
ppca_denoise_classes	filter controls	num	# eigenvecs (0 => auto for Nyström kPCA; default 160; try 128, 160)	e.g. 10
ppca_volvar	filter controls	num	# eigenvecs	e.g. 10
trajectory_denoise	filter controls	num	Number of diffusion-map components (0 => auto; default 0)	e.g. 10
trajectory_reconstruct3D	search controls	num	Flex latent dimensions	e.g. 10

Parameter newbox

Used by program	Section	Type	Parameter label	Placeholder
scale	parameter input/output	num	Scaled box size	e.g. 10

Parameter nframes

Used by program	Section	Type	Parameter label	Placeholder
print_dose_weights	parameter input/output	num	Number of frames	e.g. 10
simulate_movie	parameter input/output	num	Number of frames	e.g. 10
simulate_particles	parameter input/output	num	# of particle frames	e.g. 10

Parameter nframesgrp

Used by program	Section	Type	Parameter label	Placeholder
stackops	parameter input/output	num	Number of stack entries to group & average	e.g. 10
track_particles	search controls	num	Number of contigous frames to average	e.g. 10
tseries_make_pickavg	parameter input/output	num	# contigous frames to average	e.g. 10
tseries_motion_correct	search controls	num	# frames in time moving time window	e.g. 10

Parameter ngrow

Used by program	Section	Type	Parameter label	Placeholder
automask2D	mask controls	num	# layers to grow	e.g. 10
gen_pickrefs	mask controls	num	Automask growth layers	e.g. 10

Parameter nicedispid

Used by program	Section	Type	Parameter label	Placeholder
master	parameter input/output	hidden_int	Optics group offset delta multiplier	(empty)

Parameter ninipick

Used by program	Section	Type	Parameter label	Placeholder
preproc	parameter input/output	num	Number of micrographs to perform initial picking preprocessing on	e.g. 10

Parameter nits_per_stage

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	num	Iterations per stage	e.g. 10

Parameter nmics

Used by program	Section	Type	Parameter label	Placeholder
gen_pickrefs	parameter input/output	num	Number of micrographs to import	e.g. 10
particle_sieving	search controls	num	Max # of micrographs per chunk	e.g. 10
sieve_cavgs	parameter input/output	num	Micrographs per sieve cycle	e.g. 10

Parameter nmoldiams

Used by program	Section	Type	Parameter label	Placeholder
pick	parameter input/output	num	Number of molecular diameters to investigate	e.g. 10
pick_extract	parameter input/output	num	Number of molecular diameters to investigate	e.g. 10

Parameter noise_norm

Used by program	Section	Type	Parameter label	Placeholder
normalize	parameter input/output	binary	Noise normalize	(empty)

Parameter norm

Used by program	Section	Type	Parameter label	Placeholder
normalize	parameter input/output	binary	Normalize	(empty)

Parameter nparts

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	computer controls	num	Number of computing nodes	e.g. 10
abinitio2D_chunks	computer controls	num	Number of computing nodes	e.g. 10
abinitio2D_stream	computer controls	num	Number of computing nodes	e.g. 10
abinitio3D	computer controls	num	Number of computing nodes	e.g. 10
abinitio3D_cavgs	computer controls	num	Number of computing nodes	e.g. 10
abinitio3D_nano	computer controls	num	Number of computing nodes	e.g. 10
bootstrap_cavgs	computer controls	num	Number of computing nodes	e.g. 10
bootstrap_rec3D	computer controls	num	Number of computing nodes	e.g. 10
cls_split	computer controls	num	Number of computing nodes	e.g. 10
cluster2D_nano	computer controls	num	Number of computing nodes	e.g. 10
ctf_estimate	computer controls	num	Number of computing nodes	e.g. 10
denoise_project	computer controls	num	Number of computing nodes	e.g. 10
extract	computer controls	num	Number of computing nodes	e.g. 10
flex_analysis	computer controls	num	Number of computing nodes	e.g. 10
fractionate_movies	computer controls	num	Number of computing nodes	e.g. 10
gen_pspecs_and_thumbs	computer controls	num	Number of computing nodes	e.g. 10
make_cavgs	computer controls	num	Number of computing nodes	e.g. 10
motion_correct	computer controls	num	Number of computing nodes	e.g. 10
particle_sieving	computer controls	num	Number of chunks classified simultaneously	e.g. 10
pick	computer controls	num	Number of computing nodes	e.g. 10
pick_extract	computer controls	num	Number of computing nodes	e.g. 10
preproc	computer controls	num	Number of computing nodes	e.g. 10
preprocess	computer controls	num	Number of computing nodes	e.g. 10
prune_project	computer controls	num	Number of computing nodes	e.g. 10
reconstruct3D	computer controls	num	Number of computing nodes	e.g. 10
reextract	computer controls	num	Number of computing nodes	e.g. 10
refine3D	computer controls	num	Number of computing nodes	e.g. 10
refine3D_auto	computer controls	num	Number of computing nodes	e.g. 10
refine3D_multi	computer controls	num	Number of computing nodes	e.g. 10
refine3D_nano	computer controls	num	Number of computing nodes	e.g. 10
sample_classes	parameter input/output	num	Number of partitions in balancing	e.g. 10
selection	parameter input/output	num	Number of partitions in balancing	e.g. 10
sieve_cavgs	computer controls	num	Number of computing nodes	e.g. 10
split	computer controls	num	Number of computing nodes	e.g. 10
split_stack	parameter input/output	num	Number of parts balanced splitting of the stack	e.g. 10
trajectory_reconstruct3D	computer controls	num	Number of computing nodes	e.g. 10
tseries_motion_correct	computer controls	num	Number of computing nodes	e.g. 10

Parameter npreimages

Used by program	Section	Type	Parameter label	Placeholder
flex_analysis	filter controls	num	Representative state volumes (default 8)	e.g. 10

Parameter nptcls

Used by program	Section	Type	Parameter label	Placeholder
make_oris	parameter input/output	num	Number of per-particle orientations	e.g. 10
simulate_noise	parameter input/output	num	Number of particles	e.g. 10
simulate_particles	parameter input/output	num	Number of particles	e.g. 10

Parameter nptcls_coarse

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Target # of particles per coarse chunk	e.g. 10
sieve_cavgs	search controls	num	Target coarse-pass particle count	e.g. 10

Parameter nptcls_fine

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Target # of particles per fine chunk	e.g. 10
sieve_cavgs	search controls	num	Target fine-pass particle count	e.g. 10

Parameter nptcls_per_cls

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D_chunks	search controls	num	Number of particles per cluster	e.g. 10
analysis2D_nano	search controls	num	Number of particles per cluster	e.g. 10
check_refpick	search controls	num	Number of particles per class	e.g. 10
cluster2D_nano	search controls	num	Number of particles per cluster	e.g. 10
gen_pickrefs	search controls	num	Number of particles per cluster	e.g. 10
mini_stream	search controls	num	Number of particles per class	e.g. 10
sieve_cavgs	search controls	num	Number of particles per cluster	e.g. 10

Parameter nptcls_per_part

Used by program	Section	Type	Parameter label	Placeholder
sample_classes	parameter input/output	num	Number of ptcls per part to select when balancing	e.g. 10
selection	parameter input/output	num	Number of ptcls per part to select when balancing	e.g. 10

Parameter nran

Used by program	Section	Type	Parameter label	Placeholder
selection	parameter input/output	num	Number of random samples	e.g. 10
stackops	parameter input/output	num	Number of random samples	e.g. 10

Parameter nrestarts

Used by program	Section	Type	Parameter label	Placeholder
autorefine3D_nano	search controls	num	Number of restarts	e.g. 10

Parameter nsample

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	num	Number of particles to sample	e.g. 10
abinitio3D	search controls	num	Number of particles to sample	e.g. 10
abinitio3D_nano	search controls	num	Number of particles to sample	e.g. 10
refine3D_auto	search controls	num	Projection samples	e.g. 10
refine3D_multi	search controls	num	Particle sample target	e.g. 10
sample_classes	parameter input/output	num	Number of particles to sample	e.g. 10

Parameter nsample_coarse

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Number of particles to sample in coarse sieving	e.g. 10
sieve_cavgs	search controls	num	Coarse-pass sample count	e.g. 10

Parameter nsample_fine

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	num	Number of particles to sample in fine sieving	e.g. 10
sieve_cavgs	search controls	num	Fine-pass sample count	e.g. 10

Parameter nspace

Used by program	Section	Type	Parameter label	Placeholder
autorefine3D_nano	search controls	num	Number of projection directions	e.g. 10
denoise_project	search controls	num	Number of projection directions	e.g. 10
flex_analysis	search controls	num	Number of projection directions	e.g. 10
fsc_area_score	parameter input/output	num	Number of cone axes	e.g. 10
make_cavgs	parameter input/output	num	Number of projection directions	e.g. 10
oristats	parameter input/output	num	Number of projection directions	e.g. 10
refine3D	search controls	num	Number of projection directions	e.g. 10
refine3D_nano	search controls	num	Number of projection directions	e.g. 10
reproject	search controls	num	Number of projection directions	e.g. 10
trajectory_make_projavgs	parameter input/output	num	Number of projection directions	e.g. 10
vizoris	parameter input/output	num	Number of projection directions	e.g. 10

Parameter nspace_sub

Used by program	Section	Type	Parameter label	Placeholder
denoise_project	search controls	num	SO3 mixture subspace size	e.g. 10

Parameter nstages

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	num	Last ab initio stage to run	e.g. 10
estimate_lpstages	parameter input/output	num	Number of low-pass limit stages	e.g. 10

Parameter nstates

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	num	Number of states	e.g. 10
abinitio3D_cavgs	search controls	num	Number of states	e.g. 10
bootstrap_rec3D	search controls	num	Number of states	e.g. 10
make_oris	parameter input/output	num	Number of random state labels	e.g. 10
noisevol	parameter input/output	num	Number states	e.g. 10
oriops	parameter input/output	num	Number of random state labels	e.g. 10
ptcl3D_state_consensus	search controls	num	Number of states	e.g. 10
refine3D	search controls	num	Number of states	e.g. 10
refine3D_multi	search controls	num	Number of states	e.g. 10
trajectory_reconstruct3D	search controls	num	Number of states	e.g. 10

Parameter nsubcls_max

Used by program	Section	Type	Parameter label	Placeholder
cls_split	parameter input/output	num	Maximum subclass trial count in auto mode (default 10)	e.g. 10

Parameter nsubcls_min

Used by program	Section	Type	Parameter label	Placeholder
cls_split	parameter input/output	num	Minimum subclass trial count in auto mode (default 3)	e.g. 10

Parameter nthr

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
abinitio2D_chunks	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
abinitio2D_stream	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
abinitio3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
abinitio3D_cavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
abinitio3D_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
analysis2D_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
assign_optics	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
atoms_register	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
atoms_stats	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
auto_spher_mask	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
automask	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
automask2D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
autorefine3D_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
binarize	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
bootstrap_cavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
bootstrap_rec3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cavgseoproc_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cavgsproc_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
center	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
center2D_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
check_refpick	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cls_split	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cluster2D_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cluster_cavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cluster_cavgs_selection	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
cluster_stack	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
conv_atom_denoise	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
crys_score	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ctf_correct	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ctf_estimate	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ctfops	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
denoise_project	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
detect_atoms	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
dock_volpair	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
estimate_diam	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
extract	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
filter	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
flex_analysis	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
fractionate_movies	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
fsc	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
fsc_area_score	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
gen_pickrefs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
gen_pspecs_and_thumbs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
graphene_subtr	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
icm2D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
icm3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
make_cavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
make_oris	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
mask	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
match_cavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
match_stacks	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
mini_stream	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
model_cavgs_rejection	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
motion_correct	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
normalize	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
nu_filt3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
oristats	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
particle_sieving	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
pick	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
pick_extract	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
postprocess	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ppca_denoise	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ppca_denoise_classes	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ppca_volvar	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
preproc	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
preprocess	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
ptclsproc_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
reconstruct3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
reconstruct3D_pcg	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
reextract	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
refine3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
refine3D_auto	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
refine3D_multi	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
refine3D_nano	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
reproject	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
sample_classes	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
scale	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
sieve_cavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
simulate_movie	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
simulate_nanoparticle	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
simulate_particles	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
stackops	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
symaxis_search	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
symmetrize_map	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
symmetry_test	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
track_particles	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
trajectory_denoise	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
trajectory_make_projavgs	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
trajectory_reconstruct3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
tseries_extractor	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
tseries_make_pickavg	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
tseries_motion_correct	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
tseries_prep4tracking	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
uniform_filter2D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
uniform_filter3D	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
validate_cavgs_vs_model	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
volanalyze	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
volcluster	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10
volops	computer controls	num	Number of threads per computing node, give 0 if unsure	e.g. 10

Parameter nthr_ini3D

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	computer controls	num	Number of threads for ini3D phase, give 0 if unsure	e.g. 10

Parameter nu_refine

Used by program	Section	Type	Parameter label	Placeholder
refine3D	filter controls	binary	NU resolution expansion refinement	(empty)
refine3D_auto	filter controls	binary	NU resolution expansion refinement	(empty)

Parameter numlen

Used by program	Section	Type	Parameter label	Placeholder
preprocess	parameter input/output	num	Length of number string	e.g. 10

Parameter nxpatch

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	search controls	num	# of patches along x-axis	e.g. 10
preprocess	search controls	num	# of patches along x-axis	e.g. 10
tseries_make_pickavg	search controls	num	# of patches along x-axis	e.g. 10
tseries_motion_correct	search controls	num	# of patches along x-axis	e.g. 10

Parameter nypatch

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	search controls	num	# of patches along y-axis	e.g. 10
preprocess	search controls	num	# of patches along y-axis	e.g. 10
tseries_make_pickavg	search controls	num	# of patches along y-axis	e.g. 10
tseries_motion_correct	search controls	num	# of patches along y-axis	e.g. 10

Parameter objfun

Used by program	Section	Type	Parameter label	Placeholder
reconstruct3D_pcg	parameter input/output	multi	Objective function	(empty)
refine3D	search controls	multi	Objective function	(empty)

Parameter objfun_den

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	binary	Denoised objective	(empty)
refine3D	search controls	binary	Denoised objective	(empty)

Parameter objfun_den_w

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	num	Denoised objective weight	e.g. 10
refine3D	search controls	num	Denoised objective weight	e.g. 10

Parameter offset

Used by program	Section	Type	Parameter label	Placeholder
track_particles	search controls	num	Shift half-width search bound	e.g. 10

Parameter optics_dir

Used by program	Section	Type	Parameter label	Placeholder
gen_pickrefs	file input/output	dir	Target directory for optics import	e.g. optics_assignment

Parameter optics_offset

Used by program	Section	Type	Parameter label	Placeholder
assign_optics_groups	parameter input/output	num	Numbering offset to apply to optics groups	e.g. 10
export_relion	parameter input/output	num	Offset to apply to optics group numbering	e.g. 10

Parameter oritab

Used by program	Section	Type	Parameter label	Placeholder
center	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
ctfops	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
import_particles	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
mask	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
oriops	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
oristats	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
reproject	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
simulate_particles	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
stackops	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt
vizoris	file input/output	file	Orientation and CTF parameter file	e.g. oritab.txt

Parameter oritab2

Used by program	Section	Type	Parameter label	Placeholder
oristats	file input/output	file	2nd orientation and CTF parameter file	e.g. oritab2.txt

Parameter oritype

Used by program	Section	Type	Parameter label	Placeholder
cls_split	parameter input/output	multi	Particle type to split	(empty)
flex_analysis	parameter input/output	str	Particle orientation segment	e.g. value
make_oris	parameter input/output	multi	Oritype segment in project	(empty)
oriops	parameter input/output	multi	Oritype segment in project	(empty)
oristats	parameter input/output	multi	Oritype segment in project	(empty)
print_project_field	parameter input/output	multi	Oritype segment in project	(empty)
reconstruct3D_pcg	parameter input/output	multi	Oritype segment in project	(empty)
reextract	parameter input/output	multi	Oritype segment in project	(empty)
replace_project_field	parameter input/output	multi	Oritype segment in project	(empty)
selection	parameter input/output	multi	Oritype segment in project	(empty)
vizoris	parameter input/output	multi	Oritype segment in project	(empty)

Parameter osmpl_fac

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_cavgs	parameter input/output	num	Oversampling factor	e.g. 10

Parameter outfile

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_rec3D	file input/output	file	Resolution output prefix	e.g. resolution
center	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
dock_volpair	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
flex_analysis	file input/output	file	Discrete-state project	e.g. flex_cluster_states.simple
make_oris	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
mask	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
oriops	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
simulate_particles	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
stackops	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
volcluster	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt
volops	file input/output	file	Output orientation and CTF parameter file	e.g. orientations.txt

Parameter outside

Used by program	Section	Type	Parameter label	Placeholder
extract	parameter input/output	binary	Extract outside stage boundaries	(empty)
reextract	parameter input/output	binary	Extract outside stage boundaries	(empty)

Parameter outstk

Used by program	Section	Type	Parameter label	Placeholder
convert	image input/output	file	Output stack name	e.g. output.mrcs
ctf_correct	image input/output	file	Output stack name	e.g. output.mrcs
ctfops	image input/output	file	Output stack name	e.g. output.mrcs
filter	image input/output	file	Output stack name	e.g. output.mrcs
graphene_subtr	image input/output	file	Output stack name	e.g. output.mrcs
ppca_denoise	image input/output	file	Output stack name	e.g. output.mrcs
ppca_volvar	image input/output	file	Output stack name	e.g. output.mrcs
reproject	image input/output	file	Output stack name	e.g. output.mrcs
scale	image input/output	file	Output stack name	e.g. output.mrcs
simulate_particles	image input/output	file	Output stack name	e.g. output.mrcs
stack	image input/output	file	Output stack name	e.g. output.mrcs
stackops	image input/output	file	Output stack name	e.g. output.mrcs
trajectory_denoise	image input/output	file	Output stack name	e.g. output.mrcs

Parameter outvol

Used by program	Section	Type	Parameter label	Placeholder
conv_atom_denoise	image input/output	file	Output volume name	e.g. volume.mrc
convert	image input/output	file	Output volume name	e.g. volume.mrc
dock_volpair	image input/output	file	Output volume name	e.g. volume.mrc
filter	image input/output	file	Output volume name	e.g. volume.mrc
flex_analysis	image input/output	file	Output volume name	e.g. volume.mrc
nu_filt3D	image input/output	file	Output volume name	e.g. volume.mrc
pdb2mrc	image input/output	file	Output volume name	e.g. volume.mrc
scale	image input/output	file	Output volume name	e.g. volume.mrc
simulate_nanoparticle	image input/output	file	Output volume name	e.g. volume.mrc
symmetrize_map	image input/output	file	Output volume name	e.g. volume.mrc
trajectory_reconstruct3D	image input/output	file	Output volume name	e.g. volume.mrc
volops	image input/output	file	Output volume name	e.g. volume.mrc

Parameter overlap

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	num	Convergence overlap target	e.g. 10
abinitio3D_cavgs	search controls	num	Convergence overlap target	e.g. 10
autorefine3D_nano	search controls	num	Convergence overlap target	e.g. 10
refine3D_multi	search controls	num	State-overlap convergence target	e.g. 10

Parameter particle_density

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	multi	Particle density in micrographs	(empty)
pick	search controls	multi	Particle density in micrographs	(empty)

Parameter pca_mode

Used by program	Section	Type	Parameter label	Placeholder
cls_split	filter controls	multi	Class split embedding method	(empty)
ppca_denoise	filter controls	multi	PCA methods: PPCA, PPCA plus residual kPCA, standard SVD PCA, kernel PCA, or diffusion maps	(empty)
ppca_denoise_classes	filter controls	multi	PCA methods: PPCA, standard SVD PCA or kernel PCA	(empty)
trajectory_denoise	filter controls	multi	PCA methods: diffusion maps, PPCA, PPCA plus residual kPCA, standard SVD PCA, or kernel PCA	(empty)

Parameter pcgop

Used by program	Section	Type	Parameter label	Placeholder
reconstruct3D_pcg	search controls	multi	PCG normal operator	(empty)

Parameter pcontrast

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	multi	Input particle contrast	(empty)
extract	parameter input/output	multi	Input particle contrast	(empty)
mini_stream	parameter input/output	multi	Input particle contrast	(empty)
pick	parameter input/output	multi	Input particle contrast	(empty)
pick_extract	parameter input/output	multi	Input particle contrast	(empty)
reextract	parameter input/output	multi	Input particle contrast	(empty)

Parameter pdbfile

Used by program	Section	Type	Parameter label	Placeholder
atoms_stats	file input/output	file	PDB	e.g. molecule.pdb
mask	mask controls	file	PDB for 3D envelope masking	e.g. molecule.pdb
model_validate	file input/output	file	PDB input coordinates file	e.g. molecule.pdb
pdb2mrc	file input/output	file	PDB input coordinates file	e.g. molecule.pdb
simulate_nanoparticle	file input/output	file	PDB	e.g. molecule.pdb

Parameter pdbfile2

Used by program	Section	Type	Parameter label	Placeholder
atoms_stats	file input/output	file	PDB	e.g. molecule.pdb

Parameter pdbfiles

Used by program	Section	Type	Parameter label	Placeholder
atoms_rmsd	file input/output	file	txt	e.g. pdb_files.txt
core_atoms_analysis	file input/output	file	txt	e.g. pdb_files.txt

Parameter pdbout

Used by program	Section	Type	Parameter label	Placeholder
pdb2mrc	file input/output	file	Output PDB volume-centered molecule	e.g. output.pdb
simulate_nanoparticle	file input/output	file	Output PDB	e.g. output.pdb

Parameter period

Used by program	Section	Type	Parameter label	Placeholder
tseries_make_pickavg	parameter input/output	num	Period for repeated averaging windows	e.g. 10

Parameter pgrp

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	str	Point-group symmetry	e.g. value
abinitio3D_cavgs	search controls	str	Point-group symmetry	e.g. value
autorefine3D_nano	search controls	str	Point-group symmetry	e.g. value
bootstrap_rec3D	search controls	str	Point-group symmetry	e.g. value
cavgseoproc_nano	search controls	str	Point-group symmetry	e.g. value
cavgsproc_nano	search controls	str	Point-group symmetry	e.g. value
make_oris	parameter input/output	str	Point-group symmetry	e.g. value
oriops	parameter input/output	str	Point-group symmetry	e.g. value
oristats	parameter input/output	str	Point-group symmetry	e.g. value
pick_extract	search controls	str	Point-group symmetry	e.g. value
ptclsproc_nano	search controls	str	Point-group symmetry	e.g. value
reconstruct3D	search controls	str	Point-group symmetry	e.g. value
refine3D	search controls	str	Point-group symmetry	e.g. value
refine3D_auto	search controls	str	Point-group symmetry	e.g. value
refine3D_multi	search controls	str	Point-group symmetry	e.g. value
refine3D_nano	search controls	str	Point-group symmetry	e.g. value
reproject	search controls	str	Point-group symmetry	e.g. value
simulate_particles	search controls	str	Point-group symmetry	e.g. value
symaxis_search	search controls	str	Point-group symmetry	e.g. value
symmetrize_map	search controls	str	Point-group symmetry	e.g. value
trajectory_reconstruct3D	search controls	str	Point-group symmetry	e.g. value
validate_cavgs_vs_model	search controls	str	Point-group symmetry	e.g. value
vizoris	parameter input/output	str	Point-group symmetry	e.g. value

Parameter pgrp_start

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	str	Initital point-group symmetry	e.g. value
abinitio3D_cavgs	search controls	str	Initital point-group symmetry	e.g. value

Parameter phrand

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	binary	Phase randomization	(empty)

Parameter phshift_max

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	num	Maximum CTF phase shift	e.g. 10
ctf_estimate	search controls	num	Maximum CTF phase shift	e.g. 10
mini_stream	search controls	num	Maximum CTF phase shift	e.g. 10
preproc	search controls	num	Maximum CTF phase shift	e.g. 10
preprocess	search controls	num	Maximum CTF phase shift	e.g. 10

Parameter phshift_min

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	num	Minimum CTF phase shift	e.g. 10
ctf_estimate	search controls	num	Minimum CTF phase shift	e.g. 10
mini_stream	search controls	num	Minimum CTF phase shift	e.g. 10
preproc	search controls	num	Minimum CTF phase shift	e.g. 10
preprocess	search controls	num	Minimum CTF phase shift	e.g. 10

Parameter phshift_step

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	num	CTF phase-shift step	e.g. 10
ctf_estimate	search controls	num	CTF phase-shift step	e.g. 10
mini_stream	search controls	num	CTF phase-shift step	e.g. 10
preproc	search controls	num	CTF phase-shift step	e.g. 10
preprocess	search controls	num	CTF phase-shift step	e.g. 10

Parameter phshiftunit

Used by program	Section	Type	Parameter label	Placeholder
import_particles	parameter input/output	multi	Phase-shift unit	(empty)

Parameter pick_roi

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	search controls	binary	Artefactual regions exclusion(new picker only)	(empty)
gen_pickrefs	search controls	binary	Artefactual regions exclusion(new picker only)	(empty)
mini_stream	search controls	binary	Artefactual regions exclusion(new picker only)	(empty)
pick	search controls	binary	Artefactual regions exclusion(new picker only)	(empty)
pick_extract	search controls	binary	Artefactual regions exclusion(new picker only)	(empty)

Parameter picker

Used by program	Section	Type	Parameter label	Placeholder
pick	parameter input/output	multi	Which picker to use	(empty)

Parameter pickrefs

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	image input/output	file	Stack of class-averages/reprojections for picking	e.g. pickrefs.mrc
master	image input/output	file	2D averages for use as picking references (optional)	e.g. pickrefs.mrc
pick	image input/output	file	Stack of class-averages/reprojections for picking	e.g. pickrefs.mrc
pick_extract	image input/output	file	Stack of class-averages/reprojections for picking	e.g. pickrefs.mrc

Parameter plaintexttab

Used by program	Section	Type	Parameter label	Placeholder
import_particles	file input/output	file	Plain text file of input parameters	e.g. params.txt

Parameter platonic

Used by program	Section	Type	Parameter label	Placeholder
symmetry_test	search controls	binary	Search for Platonic symmetries	(empty)

Parameter plot_key

Used by program	Section	Type	Parameter label	Placeholder
print_project_field	parameter input/output	string	plot plot_key on , sort on x	e.g. value

Parameter positive

Used by program	Section	Type	Parameter label	Placeholder
automask2D	mask controls	binary	Consider only positive pixels	(empty)

Parameter postprocess

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_rec3D	filter controls	binary	Postprocess final map	(empty)
reconstruct3D	filter controls	binary	Postprocess final map	(empty)

Parameter ppca_kpca_resid_alpha

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise	filter controls	num	Residual hybrid damping (0 => PPCA only; default 0.5)	e.g. 10
trajectory_denoise	filter controls	num	Residual hybrid damping (0 => PPCA only; default 0.5)	e.g. 10

Parameter pre_norm

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise_classes	parameter input/output	binary	Pre-normalize images	(empty)

Parameter preimage_mode

Used by program	Section	Type	Parameter label	Placeholder
flex_analysis	filter controls	multi	Diffusion-map output mode	(empty)

Parameter preimage_ndim

Used by program	Section	Type	Parameter label	Placeholder
flex_analysis	filter controls	num	Local-linear pre-image design dimension (default 2)	e.g. 10

Parameter prob_neigh_mode

Used by program	Section	Type	Parameter label	Placeholder
refine3D	search controls	multi	Prob-neigh neighborhood mode	(empty)
refine3D_multi	search controls	multi	Prob-neigh neighborhood mode	(empty)

Parameter projfile

Used by program	Section	Type	Parameter label	Placeholder
estimate_lpstages	file input/output	file	Project file	e.g. input.simple
export_manifoldem_starproject	file input/output	file	Project file	e.g. input.simple
extract_subproj	file input/output	file	Project file	e.g. input.simple
extract_substk	file input/output	file	Project file	e.g. input.simple
map_params_from_den	file input/output	file	Project file	e.g. input.simple
match_cavgs	file input/output	file	Project file	e.g. input.simple
new_project	file input/output	file	Project file	e.g. input.simple
ptcl3D_state_consensus	file input/output	file	Project file	e.g. input.simple
replace_project_field	file input/output	file	Project file	e.g. input.simple
scale	file input/output	file	Project file	e.g. input.simple
selection	file input/output	file	Project file	e.g. input.simple
update_project	file input/output	file	Project file	e.g. input.simple
validate_projfile	file input/output	file	Project file	e.g. input.simple
write_mic_filetab	file input/output	file	Project file	e.g. input.simple

Parameter projfile_den

Used by program	Section	Type	Parameter label	Placeholder
map_params_from_den	file input/output	file	Denoised child project file	e.g. input.simple

Parameter projfile_merged

Used by program	Section	Type	Parameter label	Placeholder
merge_projects	file input/output	file	Merged output project file	e.g. input.simple

Parameter projfile_orig

Used by program	Section	Type	Parameter label	Placeholder
unbootstrap_cavgs	file input/output	file	Original project file	e.g. input.simple

Parameter projfile_raw

Used by program	Section	Type	Parameter label	Placeholder
map_params_from_den	file input/output	file	Raw project file	e.g. input.simple

Parameter projfile_ref

Used by program	Section	Type	Parameter label	Placeholder
match_cavgs	file input/output	file	Reference project file	e.g. input.simple

Parameter projfile_target

Used by program	Section	Type	Parameter label	Placeholder
replace_project_field	file input/output	file	Another project file	e.g. input.simple

Parameter projname

Used by program	Section	Type	Parameter label	Placeholder
new_project	parameter input/output	str	Project name	e.g. value

Parameter projrec

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	binary	Projection-direction reconstruction	(empty)
reconstruct3D	search controls	binary	Projection-direction reconstruction	(empty)
refine3D	search controls	binary	Projection-direction reconstruction	(empty)

Parameter projstats

Used by program	Section	Type	Parameter label	Placeholder
oristats	parameter input/output	binary	Projection statistics	(empty)

Parameter projtab

Used by program	Section	Type	Parameter label	Placeholder
merge_projects	file input/output	file	Project file table	e.g. projtab.txt
ptcl3D_state_consensus	file input/output	file	Project file table	e.g. projtab.txt

Parameter prune

Used by program	Section	Type	Parameter label	Placeholder
cluster_cavgs	parameter input/output	binary	Automated particles pruning	(empty)
map_cavgs_selection	parameter input/output	binary	Automated particles pruning	(empty)
match_cavgs	parameter input/output	binary	Automated particles pruning	(empty)
model_cavgs_rejection	parameter input/output	binary	Automated particles pruning	(empty)
ptcl3D_state_consensus	parameter input/output	binary	Automated particles pruning	(empty)
select_clusters	parameter input/output	binary	Automated particles pruning	(empty)
selection	parameter input/output	binary	Automated particles pruning	(empty)

Parameter pspecsz

Used by program	Section	Type	Parameter label	Placeholder
check_refpick	parameter input/output	num	Size of power spectrum	e.g. 10
ctf_estimate	parameter input/output	num	Size of power spectrum	e.g. 10
gen_pspecs_and_thumbs	parameter input/output	num	Size of power spectrum	e.g. 10
mini_stream	parameter input/output	num	Size of power spectrum	e.g. 10
motion_correct	parameter input/output	num	Size of power spectrum	e.g. 10
preproc	parameter input/output	num	Size of power spectrum	e.g. 10
preprocess	parameter input/output	num	Size of power spectrum	e.g. 10

Parameter ptcl_src

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	multi	Particle source	(empty)
reconstruct3D	search controls	multi	Particle source	(empty)
refine3D	search controls	multi	Particle source	(empty)
refine3D_auto	search controls	multi	Particle source	(empty)
refine3D_multi	search controls	multi	Particle source	(empty)

Parameter qsys_name

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	multi	Queue system kind	(empty)
update_project	computer controls	multi	Queue system kind	(empty)

Parameter qsys_partition

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	str	Name of SLURM/PBS/LSF partition	e.g. value
update_project	computer controls	str	Name of SLURM/PBS/LSF partition	e.g. value

Parameter qsys_qos

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	str	Schedule priority	e.g. value
update_project	computer controls	str	Schedule priority	e.g. value

Parameter qsys_reservation

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	str	Name of reserved partition	e.g. value
update_project	computer controls	str	Name of reserved partition	e.g. value

Parameter quality_context

Used by program	Section	Type	Parameter label	Placeholder
model_cavgs_rejection	parameter input/output	multi	Class-average quality context	(empty)

Parameter quality_mode

Used by program	Section	Type	Parameter label	Placeholder
model_cavgs_rejection	parameter input/output	multi	Class-average quality mode	(empty)

Parameter quality_model

Used by program	Section	Type	Parameter label	Placeholder
model_cavgs_rejection	parameter input/output	multi	Class-average quality model	(empty)

Parameter real_filter

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	multi	Real-space filter	(empty)

Parameter ref_ind

Used by program	Section	Type	Parameter label	Placeholder
volanalyze	parameter input/output	num	Reference volume index	e.g. 10

Parameter refine

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	multi	Refinement mode	(empty)
abinitio2D_chunks	search controls	multi	Refinement mode	(empty)
refine3D	search controls	multi	Refinement mode	(empty)
refine3D_nano	search controls	multi	Refinement mode	(empty)

Parameter refs

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_cavgs	image input/output	file	Bootstrap reference class averages	e.g. references.mrc
make_cavgs	image input/output	file	Output 2D references	e.g. references.mrc
particle_sieving	search controls	file	Reference class averages to initialise size compatibility model	e.g. references.mrc

Parameter reliongroups

Used by program	Section	Type	Parameter label	Placeholder
export_relion	parameter input/output	num	Number of Relion groups based on defocus	e.g. 10

Parameter remap_cls

Used by program	Section	Type	Parameter label	Placeholder
make_cavgs	parameter input/output	binary	Whether to remap 2D clusters	(empty)

Parameter res_target

Used by program	Section	Type	Parameter label	Placeholder
refine3D_auto	filter controls	num	Resolution target (in A)	e.g. 10

Parameter res_threshold

Used by program	Section	Type	Parameter label	Placeholder
selection	parameter input/output	num	Class resolution threshold	e.g. 10

Parameter rmsd_file

Used by program	Section	Type	Parameter label	Placeholder
atoms_stats	file input/output	file	bin	e.g. atom_rmsd.bin

Parameter roavg

Used by program	Section	Type	Parameter label	Placeholder
estimate_diam	parameter input/output	binary	Rotationally average	(empty)
stackops	parameter input/output	binary	Rotationally average	(empty)

Parameter rtol

Used by program	Section	Type	Parameter label	Placeholder
reconstruct3D_pcg	filter controls	num	PCG relative residual tolerance	e.g. 10

Parameter scale

Used by program	Section	Type	Parameter label	Placeholder
scale	parameter input/output	num	Scaling ratio	e.g. 10

Parameter script

Used by program	Section	Type	Parameter label	Placeholder
analysis2D_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
autorefine3D_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
cavgseoproc_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
cavgsproc_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
center2D_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
cluster2D_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
ptclsproc_nano	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)
validate_cavgs_vs_model	computer controls	binary	Generate script for shared-mem exec on cluster	(empty)

Parameter select_flag

Used by program	Section	Type	Parameter label	Placeholder
select_clusters	parameter input/output	multi	flag to use for selection	(empty)

Parameter sherr

Used by program	Section	Type	Parameter label	Placeholder
make_oris	parameter input/output	num	Shift error half-width	e.g. 10
oriops	parameter input/output	num	Shift error half-width	e.g. 10
simulate_particles	parameter input/output	num	Shift error half-width	e.g. 10

Parameter sigma

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	num	sigma, for Gaussian generation	e.g. 10

Parameter sigma_est

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	multi	Sigma estimation method	(empty)
refine3D	search controls	multi	Sigma estimation method	(empty)
refine3D_auto	search controls	multi	Sigma estimation method	(empty)
refine3D_multi	search controls	multi	Sigma estimation method	(empty)
refine3D_nano	search controls	multi	Sigma estimation method	(empty)

Parameter single_pass

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	str	Coarse pass only	e.g. value
sieve_cavgs	search controls	binary	Run coarse sieving pass only	(empty)

Parameter skip_rejection

Used by program	Section	Type	Parameter label	Placeholder
cluster_cavgs	search controls	binary	Skip class-average rejection	(empty)

Parameter smpd

Used by program	Section	Type	Parameter label	Placeholder
atoms_rmsd	parameter input/output	num	Sampling distance	e.g. 10
atoms_stats	parameter input/output	num	Sampling distance	e.g. 10
auto_spher_mask	parameter input/output	num	Sampling distance	e.g. 10
automask	parameter input/output	num	Sampling distance	e.g. 10
automask2D	parameter input/output	num	Sampling distance	e.g. 10
autorefine3D_nano	parameter input/output	num	Sampling distance	e.g. 10
cavgseoproc_nano	parameter input/output	num	Sampling distance	e.g. 10
cavgsproc_nano	parameter input/output	num	Sampling distance	e.g. 10
center	parameter input/output	num	Sampling distance	e.g. 10
check_refpick	parameter input/output	num	Sampling distance	e.g. 10
cif2mrc	parameter input/output	num	Sampling distance	e.g. 10
conv_atom_denoise	parameter input/output	num	Sampling distance	e.g. 10
core_atoms_analysis	parameter input/output	num	Sampling distance	e.g. 10
crys_score	parameter input/output	num	Sampling distance	e.g. 10
ctf_correct	parameter input/output	num	Sampling distance	e.g. 10
ctfops	parameter input/output	num	Sampling distance	e.g. 10
detect_atoms	parameter input/output	num	Sampling distance	e.g. 10
dock_volpair	parameter input/output	num	Sampling distance	e.g. 10
estimate_diam	parameter input/output	num	Sampling distance	e.g. 10
filter	parameter input/output	num	Sampling distance	e.g. 10
fsc	parameter input/output	num	Sampling distance	e.g. 10
fsc_area_score	parameter input/output	num	Sampling distance	e.g. 10
graphene_subtr	parameter input/output	num	Sampling distance	e.g. 10
icm2D	parameter input/output	num	Sampling distance	e.g. 10
icm3D	parameter input/output	num	Sampling distance	e.g. 10
import_cavgs	parameter input/output	num	Sampling distance	e.g. 10
import_movies	parameter input/output	num	Sampling distance	e.g. 10
import_particles	parameter input/output	num	Sampling distance	e.g. 10
import_trajectory	parameter input/output	num	Sampling distance	e.g. 10
mask	parameter input/output	num	Sampling distance	e.g. 10
master	parameter input/output	float	Pixel size (A)	e.g. 10
mini_stream	parameter input/output	num	Sampling distance	e.g. 10
model_validate	parameter input/output	num	Sampling distance	e.g. 10
noisevol	parameter input/output	num	Sampling distance	e.g. 10
normalize	parameter input/output	num	Sampling distance	e.g. 10
nu_filt3D	parameter input/output	num	Sampling distance	e.g. 10
pdb2mrc	parameter input/output	num	Sampling distance	e.g. 10
ppca_denoise	parameter input/output	num	Sampling distance	e.g. 10
ppca_volvar	parameter input/output	num	Sampling distance	e.g. 10
preproc	parameter input/output	num	Sampling distance	e.g. 10
print_dose_weights	parameter input/output	num	Sampling distance	e.g. 10
print_fsc	parameter input/output	num	Sampling distance	e.g. 10
print_magic_boxes	parameter input/output	num	Sampling distance	e.g. 10
ptclsproc_nano	parameter input/output	num	Sampling distance	e.g. 10
reproject	parameter input/output	num	Sampling distance	e.g. 10
scale	parameter input/output	num	Sampling distance	e.g. 10
simulate_movie	parameter input/output	num	Sampling distance	e.g. 10
simulate_nanoparticle	parameter input/output	num	Sampling distance	e.g. 10
simulate_particles	parameter input/output	num	Sampling distance	e.g. 10
split	parameter input/output	num	Sampling distance	e.g. 10
stack	parameter input/output	num	Sampling distance	e.g. 10
stackops	parameter input/output	num	Sampling distance	e.g. 10
symaxis_search	parameter input/output	num	Sampling distance	e.g. 10
symmetrize_map	parameter input/output	num	Sampling distance	e.g. 10
symmetry_test	parameter input/output	num	Sampling distance	e.g. 10
trajectory_denoise	parameter input/output	num	Sampling distance	e.g. 10
tsegmaps_core_finder	parameter input/output	num	Sampling distance	e.g. 10
tseries_import	parameter input/output	num	Sampling distance	e.g. 10
uniform_filter2D	parameter input/output	num	Sampling distance	e.g. 10
uniform_filter3D	parameter input/output	num	Sampling distance	e.g. 10
validate_cavgs_vs_model	parameter input/output	num	Sampling distance	e.g. 10
volanalyze	parameter input/output	num	Sampling distance	e.g. 10
volcluster	parameter input/output	num	Sampling distance	e.g. 10
volops	parameter input/output	num	Sampling distance	e.g. 10

Parameter smpd_downscale

Used by program	Section	Type	Parameter label	Placeholder
master	parameter input/output	hidden_float	Downscaled pixel size (A)	(empty)
motion_correct	parameter input/output	num	Sampling distance after downscale	e.g. 10
preproc	parameter input/output	num	Sampling distance after downscale	e.g. 10
preprocess	parameter input/output	num	Sampling distance after downscale	e.g. 10

Parameter smpd_target

Used by program	Section	Type	Parameter label	Placeholder
model_validate	parameter input/output	num	Target sampling distance	e.g. 10

Parameter snr

Used by program	Section	Type	Parameter label	Placeholder
simulate_movie	parameter input/output	num	SNR	e.g. 10
simulate_particles	parameter input/output	num	SNR	e.g. 10
stackops	parameter input/output	num	Apply noise to give SNR	e.g. 10
volops	parameter input/output	num	SNR	e.g. 10

Parameter sort

Used by program	Section	Type	Parameter label	Placeholder
print_project_field	parameter input/output	string	sort oris on key	e.g. value

Parameter split_stage

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	num	Docked-state split stage	e.g. 10
abinitio3D_cavgs	search controls	num	Docked-state split stage	e.g. 10

Parameter starfile

Used by program	Section	Type	Parameter label	Placeholder
export_manifoldem_starproject	file input/output	file	STAR-format file name	e.g. input.star
import_particles	file input/output	file	Particles Metadata starfile	e.g. input.star
import_starproject	file input/output	file	Metadata starfile	e.g. input.star

Parameter state

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	search controls	num	Continuation state label	e.g. 10
extract_substk	parameter input/output	num	State index	e.g. 10
oriops	parameter input/output	num	State to modify	e.g. 10
postprocess	parameter input/output	num	State to postprocess	e.g. 10
prune_project	parameter input/output	num	State index	e.g. 10
reconstruct3D_pcg	parameter input/output	num	State to reconstruct	e.g. 10
selection	parameter input/output	num	State number	e.g. 10
stackops	parameter input/output	num	State index	e.g. 10

Parameter stats

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D	search controls	binary	Write class-average statistics	(empty)
info_image	parameter input/output	binary	Output statistics	(empty)
stackops	parameter input/output	binary	Provide statistics	(empty)

Parameter stepsz

Used by program	Section	Type	Parameter label	Placeholder
trajectory_reconstruct3D	parameter input/output	num	Time window size (# frames){500}	e.g. 10

Parameter stk

Used by program	Section	Type	Parameter label	Placeholder
automask2D	image input/output	file	Particle image stack	e.g. particles.mrcs
binarize	image input/output	file	Stack	e.g. particles.mrcs
center	image input/output	file	Particle image stack	e.g. particles.mrcs
cluster_cavgs	image input/output	file	Particle image stack	e.g. particles.mrcs
cluster_stack	image input/output	file	Particle image stack	e.g. particles.mrcs
convert	image input/output	file	Stack	e.g. particles.mrcs
ctfops	image input/output	file	Particle image stack	e.g. particles.mrcs
estimate_diam	image input/output	file	Particle image stack	e.g. particles.mrcs
filter	image input/output	file	Stack to filter	e.g. particles.mrcs
icm2D	image input/output	file	Odd stack	e.g. particles.mrcs
import_cavgs	image input/output	file	Stack of class averages	e.g. particles.mrcs
import_particles	image input/output	file	Stack of particles	e.g. particles.mrcs
import_trajectory	image input/output	file	Particle image stack	e.g. particles.mrcs
map_cavgs_selection	image input/output	file	Stack of cavgs to select from	e.g. particles.mrcs
mask	image input/output	file	Particle image stack	e.g. particles.mrcs
match_stacks	image input/output	file	Particle image stack	e.g. particles.mrcs
normalize	image input/output	file	Stack to normalize	e.g. particles.mrcs
ppca_denoise	image input/output	file	Stack to denoise	e.g. particles.mrcs
reimport_particles	image input/output	file	Denoised particle stack	e.g. particles.mrcs
scale	image input/output	file	Particle image stack	e.g. particles.mrcs
simulate_movie	image input/output	file	Particle image stack	e.g. particles.mrcs
split	image input/output	file	Particle image stack	e.g. particles.mrcs
stackops	image input/output	file	Particle image stack	e.g. particles.mrcs
trajectory_denoise	image input/output	file	Stack to denoise	e.g. particles.mrcs
trajectory_swap_stack	image input/output	file	Particle image stack	e.g. particles.mrcs
uniform_filter2D	image input/output	file	Odd stack	e.g. particles.mrcs

Parameter stk2

Used by program	Section	Type	Parameter label	Placeholder
icm2D	image input/output	file	Even stack	e.g. particles2.mrcs
map_cavgs_selection	image input/output	file	Stack of selected cavgs	e.g. particles2.mrcs
match_stacks	image input/output	file	Second Particle image stack	e.g. particles2.mrcs
uniform_filter2D	image input/output	file	Even stack	e.g. particles2.mrcs

Parameter stk_backgr

Used by program	Section	Type	Parameter label	Placeholder
graphene_subtr	image input/output	file	background power spectra stack, eg NP_X_background_pspec.mrc	e.g. background_pspec.mrcs

Parameter stk_den

Used by program	Section	Type	Parameter label	Placeholder
import_particles	image input/output	file	Denoised particle image stack	e.g. denoised.mrcs

Parameter stk_traj

Used by program	Section	Type	Parameter label	Placeholder
graphene_subtr	image input/output	file	Tracked NP image stack	e.g. trajectory.mrcs

Parameter stktab

Used by program	Section	Type	Parameter label	Placeholder
import_particles	file input/output	file	List of per-micrograph particle stacks	e.g. stktab.txt
info_stktab	file input/output	file	List of per-micrograph particle stacks	e.g. stktab.txt

Parameter stktab_den

Used by program	Section	Type	Parameter label	Placeholder
import_particles	file input/output	file	List of denoised particle stacks	e.g. stktab_den.txt

Parameter subprojname

Used by program	Section	Type	Parameter label	Placeholder
extract_subproj	parameter input/output	str	Subproject name	e.g. value

Parameter symrnd

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	binary	Randomize over subgroubs of point-group	(empty)

Parameter taper_edges

Used by program	Section	Type	Parameter label	Placeholder
mask	mask controls	binary	Taper edges	(empty)

Parameter tester

Used by program	Section	Type	Parameter label	Placeholder
track_particles	parameter input/output	multi	Write periodic tester-mode outputs	(empty)

Parameter thres

Used by program	Section	Type	Parameter label	Placeholder
automask	mask controls	num	Volume threshold	e.g. 10
master	parameter input/output	hidden_float	Distance threshold for peak picking(A)	(empty)
pick_extract	search controls	num	Peak-picking distance threshold	e.g. 10

Parameter tilt_thres

Used by program	Section	Type	Parameter label	Placeholder
assign_optics_groups	parameter input/output	num	Threshold for hierarchical clustering of beamtilts	e.g. 10
export_relion	parameter input/output	num	Distance threshold	e.g. 10
preproc	search controls	num	Threshold for hierarchical clustering of beamtilts	e.g. 10

Parameter tiltgroupmax

Used by program	Section	Type	Parameter label	Placeholder
export_relion	parameter input/output	num	Max movies in a tilt/optics group	e.g. 10

Parameter time_per_image

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	num	Time per image	e.g. 10
update_project	computer controls	num	Time per image	e.g. 10

Parameter tof

Used by program	Section	Type	Parameter label	Placeholder
fractionate_movies	parameter input/output	num	Final frame	e.g. 10

Parameter top

Used by program	Section	Type	Parameter label	Placeholder
extract_subproj	parameter input/output	num	To index	e.g. 10
extract_substk	parameter input/output	num	To index	e.g. 10
scale	parameter input/output	num	Last stack index	e.g. 10
stackops	parameter input/output	num	To particle index	e.g. 10
trajectory_reconstruct3D	parameter input/output	num	To particle index	e.g. 10

Parameter total_dose

Used by program	Section	Type	Parameter label	Placeholder
master	parameter input/output	float	Total exposure dose (e/A2)	e.g. 10
motion_correct	parameter input/output	num	Total exposure dose (e/Ang^2)	e.g. 10
preproc	parameter input/output	num	Total exposure dose (e/Ang^2)	e.g. 10
preprocess	parameter input/output	num	Total exposure dose (e/Ang^2)	e.g. 10
print_dose_weights	parameter input/output	num	Total exposure dose (e/Ang^2)	e.g. 10

Parameter transp_pca

Used by program	Section	Type	Parameter label	Placeholder
ppca_denoise_classes	filter controls	binary	transpose for pixel-wise learning	(empty)

Parameter trs

Used by program	Section	Type	Parameter label	Placeholder
autorefine3D_nano	search controls	num	Maximum translational shift	e.g. 10
center2D_nano	search controls	num	Maximum translational shift	e.g. 10
cluster2D_nano	search controls	num	Maximum translational shift	e.g. 10
cluster_cavgs	search controls	num	Maximum translational shift	e.g. 10
cluster_cavgs_selection	search controls	num	Maximum translational shift	e.g. 10
cluster_stack	search controls	num	Maximum translational shift	e.g. 10
dock_volpair	search controls	num	Maximum translational shift	e.g. 10
match_cavgs	search controls	num	Maximum translational shift	e.g. 10
match_stacks	search controls	num	Maximum translational shift	e.g. 10
motion_correct	search controls	num	Max shift per iter in pixels{10.}	e.g. 10
preproc	search controls	num	Max shift per iter in pixels{10.}	e.g. 10
preprocess	search controls	num	Max shift per iter in pixels{10.}	e.g. 10
reconstruct3D	search controls	num	Maximum translational shift	e.g. 10
refine3D	search controls	num	Maximum translational shift	e.g. 10
refine3D_nano	search controls	num	Maximum translational shift	e.g. 10
simulate_movie	parameter input/output	num	Maximum translational shift	e.g. 10
trajectory_reconstruct3D	search controls	num	Maximum translational shift	e.g. 10
tseries_make_pickavg	search controls	num	Max shift per iter in pixels{10.}	e.g. 10
tseries_motion_correct	search controls	num	Max shift per iter in pixels{10.}	e.g. 10

Parameter trsstats

Used by program	Section	Type	Parameter label	Placeholder
oristats	parameter input/output	binary	Shift statistics	(empty)

Parameter tseries

Used by program	Section	Type	Parameter label	Placeholder
vizoris	parameter input/output	binary	Time series analysis	(empty)

Parameter update_frac

Used by program	Section	Type	Parameter label	Placeholder
refine3D	search controls	num	Fractional update per iteration	e.g. 10
refine3D_nano	search controls	num	Fractional update per iteration	e.g. 10

Parameter use_model

Used by program	Section	Type	Parameter label	Placeholder
particle_sieving	search controls	str	Use model for class-average rejection in sieving	e.g. value
sieve_cavgs	search controls	binary	Use class-average rejection model	(empty)

Parameter user_account

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	str	User account name in SLURM/PBS/LSF	e.g. value
update_project	computer controls	str	User account name in SLURM/PBS/LSF	e.g. value

Parameter user_email

Used by program	Section	Type	Parameter label	Placeholder
new_project	parameter input/output	str	Your e-mail address	e.g. value
update_project	parameter input/output	str	Your e-mail address	e.g. value

Parameter user_project

Used by program	Section	Type	Parameter label	Placeholder
new_project	computer controls	str	User project name in SLURM/PBS/LSF	e.g. value
update_project	computer controls	str	User project name in SLURM/PBS/LSF	e.g. value

Parameter view_balance

Used by program	Section	Type	Parameter label	Placeholder
flex_analysis	filter controls	binary	Correct uneven view distribution	(empty)

Parameter vis

Used by program	Section	Type	Parameter label	Placeholder
info_image	parameter input/output	binary	Visualize image	(empty)
stackops	parameter input/output	binary	Visualize stack images	(empty)

Parameter vol1

Used by program	Section	Type	Parameter label	Placeholder
abinitio3D	image input/output	file	Starting template volume	e.g. volume.mrc
atoms_stats	image input/output	file	Raw volume	e.g. volume.mrc
auto_spher_mask	image input/output	file	Odd volume	e.g. volume.mrc
automask	image input/output	file	Odd volume	e.g. volume.mrc
autorefine3D_nano	image input/output	file	FCC reference volume	e.g. volume.mrc
binarize	image input/output	file	Volume	e.g. volume.mrc
cavgseoproc_nano	image input/output	file	Volume	e.g. volume.mrc
cavgsproc_nano	image input/output	file	Volume	e.g. volume.mrc
center	image input/output	file	Volume	e.g. volume.mrc
conv_atom_denoise	image input/output	file	Volume	e.g. volume.mrc
convert	image input/output	file	Volume	e.g. volume.mrc
detect_atoms	image input/output	file	Volume	e.g. volume.mrc
dock_volpair	image input/output	file	Volume	e.g. volume.mrc
filter	image input/output	file	Volume to filter	e.g. volume.mrc
flex_analysis	image input/output	file	Mean volume	e.g. volume.mrc
fsc	image input/output	file	Odd volume	e.g. volume.mrc
fsc_area_score	image input/output	file	Odd volume	e.g. volume.mrc
icm3D	image input/output	file	Odd volume	e.g. volume.mrc
mask	image input/output	file	Volume	e.g. volume.mrc
model_validate	image input/output	file	Experimental volume	e.g. volume.mrc
normalize	image input/output	file	Volume to normalize	e.g. volume.mrc
nu_filt3D	image input/output	file	Odd volume	e.g. volume.mrc
postprocess	image input/output	file	Volume override	e.g. volume.mrc
ppca_volvar	image input/output	file	Volume	e.g. volume.mrc
refine3D	image input/output	file	Reference volume	e.g. volume.mrc
refine3D_auto	image input/output	file	Starting template volume	e.g. volume.mrc
refine3D_nano	image input/output	file	FCC reference volume	e.g. volume.mrc
reproject	image input/output	file	Volume	e.g. volume.mrc
scale	image input/output	file	Input volume	e.g. volume.mrc
simulate_particles	image input/output	file	Volume	e.g. volume.mrc
symaxis_search	image input/output	file	C1 Volume to identify symmetry axis of	e.g. volume.mrc
symmetrize_map	image input/output	file	Volume to symmetrize	e.g. volume.mrc
symmetry_test	image input/output	file	C1 Volume to identify symmetry of	e.g. volume.mrc
trajectory_reconstruct3D	image input/output	file	Mean volume for latent chunking	e.g. volume.mrc
uniform_filter3D	image input/output	file	Odd volume	e.g. volume.mrc
validate_cavgs_vs_model	image input/output	file	Volume	e.g. volume.mrc
volops	image input/output	file	Volume	e.g. volume.mrc

Parameter vol2

Used by program	Section	Type	Parameter label	Placeholder
atoms_stats	image input/output	file	Connected components volume	e.g. volume2.mrc
automask	image input/output	file	Even volume	e.g. volume2.mrc
dock_volpair	image input/output	file	Volume	e.g. volume2.mrc
fsc	image input/output	file	Even volume	e.g. volume2.mrc
fsc_area_score	image input/output	file	Even volume	e.g. volume2.mrc
icm3D	image input/output	file	Even volume	e.g. volume2.mrc
nu_filt3D	image input/output	file	Even volume	e.g. volume2.mrc
uniform_filter3D	image input/output	file	Even volume	e.g. volume2.mrc

Parameter vol3

Used by program	Section	Type	Parameter label	Placeholder
atoms_stats	image input/output	file	Volume	e.g. volume3.mrc

Parameter vol_dim

Used by program	Section	Type	Parameter label	Placeholder
pdb2mrc	parameter input/output	num	Simulated volume dimensions	e.g. 10

Parameter vol_even

Used by program	Section	Type	Parameter label	Placeholder
refine3D_nano	image input/output	file	Even volume	e.g. even.mrc

Parameter vol_odd

Used by program	Section	Type	Parameter label	Placeholder
refine3D_nano	image input/output	file	Odd volume	e.g. odd.mrc

Parameter walltime

Used by program	Section	Type	Parameter label	Placeholder
abinitio2D_chunks	computer controls	num	Walltime	e.g. 10
abinitio2D_stream	computer controls	num	Walltime	e.g. 10
new_project	computer controls	num	Walltime	e.g. 10
particle_sieving	computer controls	num	Walltime	e.g. 10
pick_extract	computer controls	num	Walltime	e.g. 10
preproc	computer controls	num	Walltime	e.g. 10
sieve_cavgs	computer controls	num	Walltime	e.g. 10
update_project	computer controls	num	Walltime	e.g. 10

Parameter wcrit

Used by program	Section	Type	Parameter label	Placeholder
motion_correct	filter controls	multi	Correlation to weights conversion scheme	(empty)
tseries_make_pickavg	filter controls	multi	Correlation to weights conversion scheme	(empty)
tseries_motion_correct	filter controls	multi	Correlation to weights conversion scheme	(empty)

Parameter which_iter

Used by program	Section	Type	Parameter label	Placeholder
bootstrap_rec3D	parameter input/output	num	Sigma iteration index	e.g. 10

Parameter width

Used by program	Section	Type	Parameter label	Placeholder
filter	filter controls	num	Cosine low-pass filter falloff	e.g. 10
mask	mask controls	num	Falloff of inner mask	e.g. 10

Parameter winsz

Used by program	Section	Type	Parameter label	Placeholder
automask2D	filter controls	num	Window size for median filter	e.g. 10
binarize	parameter input/output	num	Half-window size	e.g. 10
cluster2D_nano	search controls	num	Half-window size	e.g. 10
filter	filter controls	num	Half-window size	e.g. 10
gen_pickrefs	mask controls	num	Automask window size	e.g. 10
pick	search controls	num	Window size for sauvola	e.g. 10
stackops	parameter input/output	num	Window size for local sdev estimation	e.g. 10

Parameter xdim

Used by program	Section	Type	Parameter label	Placeholder
simulate_movie	parameter input/output	num	x-dimension	e.g. 10

Parameter xmldir

Used by program	Section	Type	Parameter label	Placeholder
assign_optics_groups	file input/output	dir	Directory containing per movie EPU XML files	e.g. /data/datasetid/xml

Parameter xmlloc

Used by program	Section	Type	Parameter label	Placeholder
export_relion	file input/output	file	Pathname of EPU XML files	e.g. /data/xml

Parameter xsh

Used by program	Section	Type	Parameter label	Placeholder
volops	parameter input/output	num	Translation along x-axis	e.g. 10

Parameter ydim

Used by program	Section	Type	Parameter label	Placeholder
simulate_movie	parameter input/output	num	y-dimension	e.g. 10

Parameter ysh

Used by program	Section	Type	Parameter label	Placeholder
volops	parameter input/output	num	Translation along y-axis	e.g. 10

Parameter zero

Used by program	Section	Type	Parameter label	Placeholder
oriops	parameter input/output	binary	Zero shifts	(empty)

Parameter zsh

Used by program	Section	Type	Parameter label	Placeholder
volops	parameter input/output	num	Translation along z-axis	e.g. 10