emda command line module¶

usage: emda [command] [arguments]

Positional Arguments¶

command: Possible choices: info, halffsc, fsc, singlemapfsc, ccmask, mapmask, modelmask, lowpass, power, bfac, resol, half2full, map2mtz, map2mtzfull, transform, mtz2map, resample, resamplemap2map, rcc, bfromcc, mmcc, fcc, mapmodelvalidate, mapmodelfsc, overlay, average, diffmap, applymask, scalemap, bestmap, predfsc, refmac, occ, mirror, model2map, composite, magref, com, fetch, pointgroup, symmetrise, rebox

Sub-commands¶

info¶

Output basic information about the map.

emda info [-h] --map MAP

Named Arguments¶

--map: input map

halffsc¶

Calculates FSC between half-maps.

emda halffsc [-h] --h1 H1 --h2 H2 [--msk MSK] [--out OUT] [--phaserand]

Named Arguments¶

--h1

input map1 map

--h2

input map2 map

--msk

input mask (mrc/map)

--out

output data table

Default: “table_variances.txt”

--phaserand

use if phase randomized FSC is calculated

Default: False

fsc¶

Calculates FSC between two maps.

emda fsc [-h] --map1 MAP1 --map2 MAP2

Named Arguments¶

--map1: input map1 map
--map2: input map2 map

singlemapfsc¶

Calculates FSC using neighbour average.

emda singlemapfsc [-h] --h1 H1 [--knl KNL]

Named Arguments¶

--h1

input map1 map

--knl

kernel radius in voxels

Default: 3

ccmask¶

Generates a mask based on halfmaps correlation.

emda ccmask [-h] --h1 H1 --h2 H2 [--knl KNL] [--itr ITR]
            [--dthreshold DTHRESHOLD]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--knl

kernel radius in voxels

Default: 4

--itr

number of dilation cycles

Default: 1

--dthreshold

threshold for density

mapmask¶

Generate a mask from a map.

emda mapmask [-h] --map MAP [--knl KNL] [--prb PRB] [--itr ITR] [--res RES]
             [--fil FIL]

Named Arguments¶

--map

input map

--knl

kernel radius in voxels

Default: 5

--prb

density cutoff probability in cumulative density function

Default: 0.99

--itr

number of dilate iterations

Default: 3

--res

lowpass resolution in Angstroms

Default: 15.0

--fil

filter type to use: ideal or butterworth

Default: “butterworth”

modelmask¶

Generate a mask from an atomic model.

emda modelmask [-h] --map MAP --mdl MDL [--atmrad ATMRAD]

Named Arguments¶

--map

input map MRC/MAP

--mdl

input atomic model PDB/CIF

--atmrad

radius of the atomic sphere in Angstroms

Default: 3.0

lowpass¶

Lowpass filter to specified resolution.

emda lowpass [-h] --map MAP --res RES [--fil FIL]

Named Arguments¶

--map

input map (mrc/map)

--res

lowpass resolution in Angstrom

--fil

filter type to use: ideal or butterworth

Default: “ideal”

power¶

Calculates power spectrum.

emda power [-h] --map MAP

Named Arguments¶

--map: input map (mrc/map)

bfac¶

Apply a B-factor on the map.

emda bfac [-h] --map MAP --bfc BFC [BFC ...] [--out]

Named Arguments¶

--map

input map (mrc/map)

--bfc

bfactor(s) to apply

--out

if use, writes out map

Default: False

resol¶

Estimates map resolution based on FSC.

emda resol [-h] --h1 H1 --h2 H2

Named Arguments¶

--h1: input halfmap1 map
--h2: input halfmap2 map

half2full¶

Combine two halfmaps to make the fullmap.

emda half2full [-h] --h1 H1 --h2 H2 [--out OUT]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--out

output map (mrc/map)

Default: “fullmap.mrc”

map2mtz¶

Convert MRC/MAP to MTZ.

emda map2mtz [-h] --map MAP [--res RES] [--out OUT]

Named Arguments¶

--map

input map (mrc/map)

--res

resolution cutoff (A). default Nyquist

--out

output map (mtz)

Default: “map2mtz.mtz”

map2mtzfull¶

Convert MRC/MAP to MTZ using half maps.

emda map2mtzfull [-h] --h1 H1 --h2 H2 [--out OUT]

Named Arguments¶

--h1

input hfmap1 (mrc/map)

--h2

input hfmap2 (mrc/map)

--out

output map (mtz)

Default: “map2mtzfull.mtz”

transform¶

Apply a transformation on the map.

emda transform [-h] --map MAP [--tra TRA [TRA ...]] [--rot ROT]
               [--axr AXR [AXR ...]] [--out OUT]

Named Arguments¶

--map

input map (mrc/map)

--tra

translation vec. in Angstrom. eg 1.0 0.0 0.0

Default: [0.0, 0.0, 0.0]

--rot

rotation in degree

Default: 0.0

--axr

rotation axis

Default: [1, 0, 0]

--out

output map (mrc/map)

Default: “transformed.mrc”

mtz2map¶

Convert MTZ to MRC/MAP.

emda mtz2map [-h] --mtz MTZ --map MAP --out OUT

Named Arguments¶

--mtz: input map (mtz)
--map: input map (mrc/map)
--out: output map (mrc/map)

resample¶

Resample a map in Fourier space.

emda resample [-h] --map MAP --pix PIX [PIX ...] --dim DIM [DIM ...]
              [--cel CEL [CEL ...]] [--out OUT]

Named Arguments¶

--map

input map (mrc/map)

--pix

target pixel size (A)

--dim

target map dimensions. e.g. 100 100 100

--cel

target cell. e.g. a b c 90 90 90

--out

output map name

Default: “resampled.mrc”

resamplemap2map¶

Resample map2 on map1.

emda resamplemap2map [-h] --map1 MAP1 --map2 MAP2 [--out OUT]

Named Arguments¶

--map1

static map (mrc/map)

--map2

map to resample (mrc/map)

--out

output map name

Default: “resampled2staticmap.mrc”

rcc¶

real space correlation

emda rcc [-h] --h1 H1 --h2 H2 [--mdl MDL] [--res RES] [--msk MSK] [--nrm]
         [--knl KNL] [--lgf LGF]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--mdl

Input model (cif/pdb)

--res

Resolution (A)

--msk

input mask (mrc/map)

--nrm

if True use normalized maps

Default: False

--knl

Kernel size (pixels)

Default: 5

--lgf

ligand description file

bfromcc¶

local b from real space correlation

emda bfromcc [-h] --h1 H1 --h2 H2 --res RES [--msk MSK] [--knl KNL]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--res

Resolution (A)

--msk

input mask (mrc/map)

--knl

Kernel size (pixels)

Default: 5

mmcc¶

real space correlation

emda mmcc [-h] --map MAP --mdl MDL --res RES [--nrm] [--msk MSK] [--knl KNL]
          [--lgf LGF]

Named Arguments¶

--map

input full/deposited map

--mdl

Input model (cif/pdb)

--res

Resolution (A)

--nrm

if use, normalized maps are used

Default: False

--msk

input mask (mrc/map)

--knl

Kernel size (pixels)

Default: 5

--lgf

ligand description file

fcc¶

Fourier space correlation

emda fcc [-h] --h1 H1 --h2 H2 [--knl KNL] [--msk MSK]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--knl

Kernel size (pixels)

Default: 5

--msk

input mask (mrc/map)

mapmodelvalidate¶

map-model validation using FSC

emda mapmodelvalidate [-h] --h1 H1 --h2 H2 --mdf MDF [--md1 MD1] [--msk MSK]
                      [--res RES] [--bfc BFC] [--lgf LGF]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--mdf

input full atomic model

--md1

input halfmap1 atomic model

--msk

input mask (mrc/map)

--res

Resolution (A)

--bfc

Overall B factor for model. default=0.0

Default: 0.0

--lgf

ligand description file

mapmodelfsc¶

map-model FSC

emda mapmodelfsc [-h] --map MAP --mdl MDL [--msk MSK] --res RES [--bfc BFC]
                 [--lgf LGF] [--phaserand]

Named Arguments¶

--map

input map

--mdl

input atomic model

--msk

input mask (mrc/map)

--res

Resolution (A)

--bfc

Overall B factor for model. default=0.0 ignored by REFMAC

Default: 0.0

--lgf

ligand description file

--phaserand

use if phase randomized FSC is calculated

Default: False

overlay¶

overlay maps

emda overlay [-h] --map MAP [MAP ...] [--msk MSK [MSK ...]]
             [--tra TRA [TRA ...]] [--rot ROT] [--axr AXR [AXR ...]]
             [--ncy NCY] [--res RES] [--fitres FITRES] [--int INT]
             [--modelres MODELRES] [--hfm] [--mod] [--usecom]

Named Arguments¶

--map

maplist for overlay

--msk

masklist for overlay

--tra

translation vector. default=[0.0, 0.0, 0.0]

Default: [0.0, 0.0, 0.0]

--rot

rotation in deg. default=0.0

Default: 0.0

--axr

rotation axis. default=[1,0,0]

Default: [1, 0, 0]

--ncy

number of fitting cycles. default=5

Default: 5

--res

starting fit resol. (A). default= 6 A

Default: 6

--fitres

final fit resol. (A). default= 0.0 A

Default: 0.0

--int

interpolation method (linear/cubic). default= linear

Default: “linear”

--modelres

model resol. (A). default= 5 A

Default: 5

--hfm

if use employ half maps

Default: False

--mod

if use calls model overlay

Default: False

--usecom

if used, center-of-mass is used to superimpose maps

Default: False

average¶

weighted average of several maps

emda average [-h] --map MAP [MAP ...] [--msk MSK [MSK ...]]
             [--tra TRA [TRA ...]] [--rot ROT] [--axr AXR [AXR ...]]
             [--ncy NCY] [--res RES] [--int INT]

Named Arguments¶

--map

maplist to average

--msk

masklist for maps

--tra

translation vec.

Default: [0.0, 0.0, 0.0]

--rot

rotation in deg

Default: 0.0

--axr

rotation axis

Default: [1, 0, 0]

--ncy

number of fitting cycles

Default: 10

--res

starting fit resol. (A)

Default: 6

--int

interpolation method ([linear]/cubic)

Default: “linear”

diffmap¶

Calculate the difference map

emda diffmap [-h] --map MAP [MAP ...] [--msk MSK [MSK ...]] --res RES
             [--mod MOD] [--fit] [--ncy NCY] [--fitres FITRES] [--usecom]
             [--usehalfmaps]

Named Arguments¶

--map

maplist to diffmap

--msk

masklist for maps

--res

resolution for difference map in Angstroms.

--mod

scaling method. norm (default) - normalized FC, ampli - amplitudes in resolution bins

Default: “norm”

--fit

if used, maps are superimposed before calculating difference map

Default: False

--ncy

number of fitting cycles

Default: 5

--fitres

final fit resol. (A). default= 0.0 A

Default: 0.0

--usecom

if used, center-of-mass is used to superimpose maps

Default: False

--usehalfmaps

if used, halfmaps are used to calculate difference map

Default: False

applymask¶

apply mask on the map

emda applymask [-h] --map MAP --msk MSK [--out OUT]

Named Arguments¶

--map

map to be masked

--msk

mask to be applied

--out

output map name

Default: “mapmasked.mrc”

scalemap¶

scale onemap to another

emda scalemap [-h] --m1 M1 --m2 M2 [--out OUT]

Named Arguments¶

--m1

input map

--m2

map to be scaled

--out

output map name

Default: “scaledmap.mrc”

bestmap¶

calculate bestmap

emda bestmap [-h] --h1 H1 --h2 H2 [--msk MSK] [--B B] [--knl KNL] [--mod MOD]
             [--out OUT]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--msk

mask to be applied

--B

relative B

--knl

kernel radius (pixels)

Default: 5

--mod

fsc type (1-resol bins, 2-local)

Default: 1

--out

output map name

Default: “bestmap.mrc”

predfsc¶

predict FSC based on # particles

emda predfsc [-h] --h1 H1 --h2 H2 [--msk MSK] [--npa NPA [NPA ...]]
             [--bfc BFC [BFC ...]]

Named Arguments¶

--h1: input halfmap1 map
--h2: input halfmap2 map
--msk: mask map
--npa: n fold of particles
--bfc: list of B factors

refmac¶

prepare data for refmac refinement

emda refmac [-h] --h1 H1 --h2 H2 [--msk MSK] [--bfc BFC [BFC ...]] [--out OUT]

Named Arguments¶

--h1

input halfmap1 map

--h2

input halfmap2 map

--msk

mask map

--bfc

b-factor list

--out

output mtz file name

Default: “output.mtz”

occ¶

overall correlation in real space

emda occ [-h] --m1 M1 --m2 M2 [--msk MSK] [--spc SPC]

Named Arguments¶

--m1

input map1 map

--m2

input map2 map

--msk

mask map

--spc

space (real/fourier) for CC calculation

Default: “real”

mirror¶

mirror the map

emda mirror [-h] --map MAP

Named Arguments¶

--map: input map

model2map¶

calculate model based map

emda model2map [-h] --mdl MDL --res RES --dim DIM [DIM ...] --cel CEL
               [CEL ...] [--lgf LGF] [--org ORG [ORG ...]] [--gemmi]

Named Arguments¶

--mdl

input atomic model

--res

Resolution (A)

--dim

map dim

--cel

cell parameters

--lgf

ligand description file

--org

map origin

--gemmi

if used, GEMMI is used instead REFMAC for structure factor calculation

Default: False

composite¶

make composite map

emda composite [-h] --map MAP [MAP ...] [--msk MSK [MSK ...]]

Named Arguments¶

--map: maplist to combine
--msk: masklist for maps

magref¶

magnification refinement

emda magref [-h] --map MAP [MAP ...] --ref REF

Named Arguments¶

--map: maplist to correct for magnification [.mrc/.map]
--ref: reference map [.mrc/.map]

com¶

center of mass

emda com [-h] --map MAP [--msk MSK]

Named Arguments¶

--map: input map (MRC/MAP)
--msk: mask to apply on the map

fetch¶

fetch EMmap and model

emda fetch [-h] --emd EMD [EMD ...] [--all]

Named Arguments¶

--emd

list of EMD entries. e.g. 3651

--all

Use to download all data (mask, map, halfdata, model)

Default: False

pointgroup¶

detect point group from the map

emda pointgroup [-h] --map MAP [MAP ...] --res RES [RES ...]
                [--emd EMD [EMD ...]] [--peak_cutoff PEAK_CUTOFF] [--use_fsc]
                [--fsc_cutoff FSC_CUTOFF] [--ang_tol ANG_TOL]

Named Arguments¶

--map

list of maps to find point groups

--res

list of resolution of maps (A)

--emd

list of emdbid of maps

--peak_cutoff

cutoff for Proshade peak height. default= 0.8

Default: 0.8

--use_fsc

if used, FSC is used in place for proshade peakheight to decide point group

Default: False

--fsc_cutoff

cutoff for Proshade peak height, default= 0.7

Default: 0.7

--ang_tol

angle tolerence between two axes for determining point group. default= 5 deg.

Default: 5.0

symmetrise¶

symmetrize map using point group symmetry

emda symmetrise [-h] --map MAP [MAP ...] --res RES [RES ...]
                [--emd EMD [EMD ...]]
                [--pointgroup POINTGROUP [POINTGROUP ...]]
                [--peak_cutoff PEAK_CUTOFF] [--use_fsc]
                [--fsc_cutoff FSC_CUTOFF] [--ang_tol ANG_TOL]

Named Arguments¶

--map

list of maps to find point groups

--res

list of resolution of maps (A)

--emd

list of emdbid of maps

--pointgroup

list of point groups

--peak_cutoff

cutoff for Proshade peak height. default= 0.8

Default: 0.8

--use_fsc

if used, FSC is used in place for proshade peakheight to decide point group

Default: False

--fsc_cutoff

cutoff for Proshade peak height, default= 0.7

Default: 0.7

--ang_tol

angle tolerence between two axes for determining point group. default= 5 deg.

Default: 5.0

rebox¶

rebox map and model using a mask

emda rebox [-h] --map MAP [MAP ...] --msk MSK [MSK ...] [--mdl MDL [MDL ...]]

Named Arguments¶

--map: list of map names for reboxing
--msk: list of mask names for reboxing
--mdl: list of model names (pdb/cif) for reboxing