e2refine_easy

and e2refine_evenodd.py. Major features of this program:

input

string

The name of the image file containing the particle data

model

string

The map to use as a starting point for refinement

OR

startfrom

string

Path to an existing refine_xx directory to continue refining from. Alternative to --input and --model.

Standard Options:

Short

Name

Type

Description

targetres

float

Target resolution in A of this refinement run. Usually works best in at least two steps (low/medium resolution, then final resolution) when starting with a poor starting model. Usually 3-4 iterations is sufficient.

speed

int

(1-7) Balances speed vs precision. Larger values sacrifice a bit of potential resolution for significant speed increases. 1 may yield slightly better results but come with a significant performance penalty. default=5

sym

bool

Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos.

breaksym

bool

If selected, reconstruction will be asymmetric with sym= specifying a known pseudosymmetry, not an imposed symmetry.

iter

int

The total number of refinement iterations to perform. Default=auto

mass

float

The ~mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass.

apix

float

The angstrom per pixel of the input particles. This argument is required if you specify the --mass argument. If unspecified (set to 0), the convergence plot is generated using either the project apix, or if not an apix of 1.

classkeep

float

The fraction of particles to keep in each class, based on the similarity score. (default=0.9 -> 90%%)

classautomask

bool

This will apply an automask to the class-average during iterative alignment for better accuracy. The final class averages are unmasked.

prethreshold

bool

Applies a threshold to the volume just before generating projections. A sort of aggressive solvent flattening for the reference.

m3dkeep

float

The fraction of slices to keep in e2make3d.py. Default=0.8 -> 80%%

m3dpostprocess

string

Default=none. An arbitrary post-processor to run after all other automatic processing. Maps are autofiltered, so a low-pass filter should not normally be used here.

-P

parallel

string

Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel

threads

int

Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful

Complete Options, including advanced options:

Short

Name

Type

Description

medianshrink

bool

Downsamples the volume by a factor of n by computing the local median

meanshrink

bool

Downsamples the volume by a factor of n by computing the local average

meanshrinkbig

bool

Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files.

meanshrinkbig

bool

Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files.

scale

bool

Rescales the image by 'n', generally used with clip option.

sym

bool

Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos

averager

bool

Averager used for --average and --sym options

clip

bool

Make the output have this size by padding/clipping. 1, 3 or 6 arguments.

fftclip

bool

Make the output have this size, rescaling by padding FFT.

process

bool

apply a processor named 'processorname' with all its parameters/values.

apix

bool

A/pixel for S scaling

origin

bool

Set the coordinates for the pixel (0,0,0) for Chimera. THIS HAS NO IMPACT ON IMAGE PROCESSING !

mult

bool

Scales the densities by a fixed number in the output

multfile

bool

Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.

matchto

bool

Match filtration of input volume to this specified volume.

outmode

bool

All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range.

outnorescale

bool

If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated.

mrc16bit

bool

(deprecated, use --outmode instead) output as 16 bit MRC file

mrc8bit

bool

(deprecated, use --outmode instead) output as 8 bit MRC file

add

bool

Adds a constant 'f' to the densities

addfile

bool

Adds the volume to another volume of identical size

calcfsc

bool

Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume.

filtertable

bool

Applies a 2 column (S,amp) file as a filter in Fourier space, assumed 0 outside the defined range.

calcsf

bool

Calculate a radial structure factor. Must specify apix.

calcradial

bool

Calculate the radial density by shell. Output file becomes a text file. 0 - mean amp, 2 - min, 3 - max, 4 - sigma

setsf

bool

Set the radial structure factor. Must specify apix.

tophalf

bool

The output only keeps the top half map

inputto1

bool

All voxels in the input file are set to 1 after reading. This can be used with mask.* processors to produce a mask file of the correct size.

icos5fhalfmap

bool

The input is the icos 5f top half map generated by the 'tophalf' option

outtype

bool

Set output image format, mrc, imagic, hdf, etc

first

bool

the first image in the input to process [0 - n-1])

trans

bool

Translate map by dx,dy,dz

resetxf

bool

Reset an existing transform matrix to the identity matrix

align

bool

Align input map to reference specified with --alignref. As with processors, a sequence of aligners is permitted

ralignzphi

string

Refine Z alignment within +-10 pixels and phi +-15 degrees (for C symmetries), specify name of alignment reference here not with --alignref

alignref

bool

Alignment reference volume. May only be specified once.

alignctod

string

Rotates a map already aligned for C symmetry so the best 2-fold is positioned for specified D symmetry. Does not impose specified symmetry.

rot

string

Rotate map. Specify az,alt,phi or convention:par=val:par=val:... eg - mrc:psi=22:theta=15:omega=7

icos5to2

bool

Rotate an icosahedral map from 5-fold on Z (EMAN standard) to 2-fold on Z (MRC standard) orientation

icos2to5

bool

Rotate an icosahedral map from 2-fold on Z (MRC standard) to 5-fold on Z (EMAN standard) orientation

last

bool

the last image in the input to process

swap

bool

Swap the byte order

average

bool

Computes the average of a stack of 3D volumes

append

bool

Append output image, i.e., do not write inplace.

ppid

int

Set the PID of the parent process, used for cross platform PPID

unstacking

bool

Process a stack of 3D images, then output a a series of numbered single image files

tomoprep

bool

Produces a special HDF file designed for rapid interactive tomography annotation. This option should be used alone.

-v

verbose

bool

verbose level [0-9], higner number means higher level of verboseness

step

string

Specify <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles

id> examples/extracthelp.py programs/e2refine_easy.py

input

string

Image stack containing phase-flipped particles used for alignment

inputavg

string

Optional file containing alternate version of the particles to use for reconstruction after alignment

model

string

The map to use as a starting point for refinement

startfrom

string

Path to an existing refine_xx directory to continue refining from. Alternative to --input and --model.

targetres

float

Target resolution in A of this refinement run. Usually works best in at least two steps (low/medium resolution, then final resolution) when starting with a poor starting model. Usually 3-4 iterations is sufficient.

speed

int

(1-7) Balances speed vs precision. Larger values sacrifice a bit of potential resolution for significant speed increases. Set to 1 when really pushing resolution. Set to 7 for initial refinements. default=5

sym

bool

Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos.

breaksym

bool

If selected, reconstruction will be asymmetric with sym= specifying a known pseudosymmetry, not an imposed symmetry.

tophat

bool

Instead of imposing a final Wiener filter, use a tophat filter (similar to Relion). Sharper features, but may exaggerate.

treeclassify

bool

Classify using a binary tree.

m3dold

bool

Use the traditional e2make3d program instead of the new e2make3dpar program

iter

int

The total number of refinement iterations to perform. Default=auto

mass

float

The ~mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass.

apix

float

The angstrom per pixel of the input particles. Normally set to 0, which will read the value from the header of the input file

sep

int

The number of classes each particle can contribute towards (normally 1). Increasing will improve SNR, but produce rotational blurring.

classkeep

float

The fraction of particles to keep in each class, based on the similarity score. (default=0.9 -> 90%%)

classautomask

bool

This will apply an automask to the class-average during iterative alignment for better accuracy. The final class averages are unmasked.

prethreshold

bool

Applies a threshold to the volume just before generating projections. A sort of aggressive solvent flattening for the reference.

eulerrefine

bool

Refines Euler angles of class-averages before reconstruction

m3dkeep

float

The fraction of slices to keep in e2make3d.py. Default=0.8 -> 80%%

m3dpostprocess

string

Default=none. An arbitrary post-processor to run after all other automatic processing. Maps are autofiltered, so a low-pass filter should not normally be used here.

-P

parallel

string

Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel

threads

int

Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful

path

string

The name of a directory where results are placed. Default = create new refine_xx

-v

verbose

int

verbose level [0-9], higner number means higher level of verboseness

usefilt

string

Specify a particle data file that has been low pass or Wiener filtered. Has a one to one correspondence with your particle data. If specified will be used in projection matching routines, and elsewhere.

automaskexpand

int

Default=boxsize/20. Specify number of voxels to expand mask before soft edge. Use this if low density peripheral features are cut off by the mask.

automask3d

string

Default=auto. Specify as a processor, eg - mask.auto3d:threshold=1.1:radius=30:nshells=5:nshellsgauss=5.

automask3d2

string

Default=none. If specified, this mask will be multiplied by the result of the first mask, eg - using mask.soft to mask out the center of a virus.

projector

bool

Default=standard. Projector to use with parameters.

orientgen

string

Default=auto. Orientation generator for projections, eg - eman:delta=5.0:inc_mirror=0:perturb=1

simalign

string

Default=auto. The name of an 'aligner' to use prior to comparing the images

simaligncmp

string

Default=auto. Name of the aligner along with its construction arguments

simralign

string

Default=auto. The name and parameters of the second stage aligner which refines the results of the first alignment

simraligncmp

string

Default=auto. The name and parameters of the comparitor used by the second stage aligner.

simcmp

string

Default=auto. The name of a 'cmp' to be used in comparing the aligned images

simmask

string

Default=auto. A file containing a single 0/1 image to apply as a mask before comparison but after alignment

shrink

int

Default=auto. Optionally shrink the input particles by an integer amount prior to computing similarity scores. For speed purposes. 0 -> no shrinking

shrinks1

int

The level of shrinking to apply in the first stage of the two-stage classification process. Default=0 (autoselect)

prefilt

bool

Default=auto. Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison. Applies both to classification and class-averaging.

cmpdiff

bool

Used only in binary tree classification. Use a mask that focus on the difference of two children.

treeincomplete

int

Used only in binary tree classification. Incompleteness of the tree on each level.Default=0

classkeepsig

bool

Change the keep ('--keep') criterion from fraction-based to sigma-based.

classiter

int

Default=auto. The number of iterations to perform.

classalign

string

Default=auto. If doing more than one iteration, this is the name and parameters of the 'aligner' used to align particles to the previous class average.

classaligncmp

string

Default=auto. This is the name and parameters of the comparitor used by the fist stage aligner.

classralign

string

Default=auto. The second stage aligner which refines the results of the first alignment in class averaging.

classraligncmp

string

Default=auto. The comparitor used by the second stage aligner in class averageing.

classaverager

string

Default=auto. The averager used to generate the class averages. Default is auto.

classcmp

string

Default=auto. The name and parameters of the comparitor used to generate similarity scores, when class averaging.

classnormproc

string

Default=auto. Normalization applied during class averaging

classrefsf

bool

Use the setsfref option in class averaging. This matches the filtration of the class-averages to the projections for easier comparison. Disabled when ampcorrect=flatten is used.

pad

int

Default=auto. To reduce Fourier artifacts, the model is typically padded by ~25 percent - only applies to Fourier reconstruction

recon

bool

Default=auto. Reconstructor to use see e2help.py reconstructors -v

m3dkeepsig

bool

Default=auto. The standard deviation alternative to the --m3dkeep argument

m3dsetsf

string

Default=auto. Name of a file containing a structure factor to apply after refinement

m3dpreprocess

string

Default=auto. Normalization processor applied before 3D reconstruction

ampcorrect

bool

Will perform amplitude correction via the specified method. 'flatten' requires a target resolution better than 8 angstroms (experimental). 'none' will disable amplitude correction (experimental).

classweight

bool

Alter the weight of each class in the reconstruction (experimental).

sqrtnorm

bool

If set, the sqrt of the number of particles in each class will be used to weight the direct fourier inversion.

lowmem

bool

Default=auto. Make limited use of memory when possible - useful on lower end machines

ppid

int

Set the PID of the parent process, used for cross platform PPID

To run this program, you would normally specify only the following options: Use these 2 when starting a new "gold standard" refinement from scratch:

Use this, when you have already achieved sufficient resolution to validate the gold-standard, and you are trying to improve resolution/quality:

Then a subset of these:

Optional:

Details about the refinement, and parameters which have automatically been selected are discussed in report/index.html