Integrated Protocols

Table of Contents

• By Categories
  • Imports
  • Micrographs
  • Particles
  • 2D
  • 3D
• By Packages
  • xmipp3 (58 protocols)
  • scipion (20 protocols)
  • spider (10 protocols)
  • relion (9 protocols)
  • eman2 (5 protocols)
  • grigoriefflab (5 protocols)
  • pytom_scipion (3 protocols)
  • bsoft (2 protocols)
  • appion (1 protocols)
  • emxlib (1 protocols)
  • resmap (1 protocols)
  • simple (1 protocols)
  • igbmc (1 protocols)
  • cryoem_scipion (1 protocols)
  • atsas (1 protocols)

By Categories

Imports

• pytom_scipion - import: Imports a particle list of subtomograms

• scipion - import averages: Imports a set of averages to the project

• scipion - import coordinates: Imports a set of coordinates

• scipion - import ctf: Imports a set of CTFs into the project

• scipion - import mask: Imports masks from existing files

• scipion - import micrographs: Imports a set of micrographs to the project

• scipion - import movies: Imports a set of movies (from direct detector cameras) to the project

• scipion - import particles: Imports a set of particles to the project

• scipion - import pdb volumes: Imports a set of PDB volumes to the project

• scipion - import tilted micrographs: Imports untilted-tilted pairs of micrographs in the project

• scipion - import volumes: Imports a set of volumes to the project

Micrographs

• grigoriefflab - Summovie: Aligns the frames of movies recorded

• grigoriefflab - Unblur: Aligns the frames of movies recorded

• grigoriefflab - ctffind: Estimates CTF on a set of micrographs

• scipion - ctf assign: Assigns a CTF estimation to a particular

• xmipp3 - ctf discrepancy: Estimates the agreement between different estimations of the CTF

• xmipp3 - ctf estimation: Estimates the CTF on a set of micrographs using Xmipp 3.1

• xmipp3 - movie alignment: Aligns movies, from direct detectors cameras, into micrographs

• xmipp3 - movie extract particles: Extracts a set of particles from each frame of a set of movies.

• xmipp3 - preprocess micrographs: Preprocesses a set of micrographs in the project. Can crop borders, remove bad pixels, etc.

Particles

• appion - dogpicker: Picks particles in a set of micrographs using Appion dogpicker

• bsoft - bfilter: Wrapper around the bfilter program

• bsoft - particle picking: Picks particles in a set of micrographs using bsoft

• eman2 - boxer: Picks particles in a set of micrographs using eman

• eman2 - sparx gaussian picker: Picks particles automatically in a set of micrographs using Sparx gaussian picker

• igbmc - auto-picking: gEMpicker is a template-based cryo-EM particle picking program that uses

• relion - auto-picking (step 1): Uses 2D class averages as templates to run auto-picking using Relion

• relion - auto-picking (step 2): Uses 2D class averages as templates to run auto-picking using Relion

• relion - particle polishing: Reconstructs a volume from a given set of particles using Relion

• relion - preprocess particles: Wrapper around the Relion preprocess program.

• scipion - extract coordinates: Extracts coordinates information from a set of particles

• scipion - import coordinates: Imports a set of coordinates

• spider - filter particles: Applies Fourier filters to an image or volume

• xmipp3 - apply 2d mask: Applies mask to a set of particles

• xmipp3 - assignment tiltpair: Determines the affine transformation from two sets of coordinates, tilted and untilted

• xmipp3 - auto-picking (step 2): Picks particles automatically in a set of micrographs using previous training

• xmipp3 - break symmetry: Classifies particles according their similarity to others in order to detect outliers

• xmipp3 - calculator2D: Applies an operation to two sets of particles

• xmipp3 - consensus picking: Estimates the agreement between different particle picking algorithms

• xmipp3 - crop/resize particles: Crops or resizes a set of particles

• xmipp3 - ctf_correct_wiener2d: Performs CTF correction by Wiener filtering

• xmipp3 - denoise particles: Removes particles' noise by filtering them. This filtering process is based on a projection over a basis created from some averages (extracted from classes). This filtering is not intended for processing particles. The huge filtering they will be passed through is known to remove part of the signal

• xmipp3 - extract particle pairs: Extracts particles from a set of tilted pairs' coordinates

• xmipp3 - extract particles: Extracts particles from a set of coordinates

• xmipp3 - filter particles: Applies Fourier filters to a set of particles

• xmipp3 - manual-picking (step 1): Picks particles in a set of micrographs using Xmipp

• xmipp3 - movie extract particles: Extracts a set of particles from each frame of a set of movies

• xmipp3 - preprocess particles: Preprocesses a set of particles. Can remove dust, normalize, apply threshold, etc.

• xmipp3 - screen particles: Classifies particles according their similarity to others in order to detect outliers

• xmipp3 - tilt pairs particle picking: Picks particles in a set of micrographs using Xmipp

2D

• relion - 2D classification: Wrapper around the class average program Relion 2D

• scipion - alignment assign: Assigns the alignment calculated for a set of particles to another set

• scipion - classes consensus: Compares two SetOfClasses

• spider - align apsr: Reference-free alignment shift and rotational alignment of an image series.

• spider - align pairwise: Reference-free alignment shift and rotational alignment of an image series

• spider - classify diday: Diday’s method, using 'CL CLA'

• spider - classify kmeans: Diday’s method, using 'CL CLA'

• spider - classify ward: Ward’s method, using 'CL HC'

• spider - custom mask: Creates a custom mask

• xmipp3 - align with cl2d: Aligns a set of particles using the CL2D algorithm

• xmipp3 - apply alignment 2d: Applies alignment parameters and produce a new set of images

• xmipp3 - cl2d: Classifies a set of images using a clustering algorithm

• xmipp3 - create 2d mask: Creates a 2D mask

• xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM)

• xmipp3 - ml2d: Performs (multi-reference) 2D alignment using

• xmipp3 - rotational spectra: Computes the rotational spectrum of the given particles

• xmipp3 - screen classes: Compares a set of classes or averages with the corresponding projections of a reference volume

3D

• atsas - convert PDB to SAXS curve: Converts a PDB file (true atoms or pseudoatoms) into a SAXS curve

• cryoem_scipion - pseudoatoms: Produces one or several initial volumes using cryoem pseudoatoms

• eman2 - initial model: Wrapper around e2initialmodel.py Eman2 program which

• eman2 - reconstruct: Wrapper around e2make3d.py Eman2 program

• eman2 - refine easy: Wrapper around e2refine_easy.py Eman2 program

• grigoriefflab - frealign: Refines a 3D map using Frealign. The algorithms implemented

• grigoriefflab - frealign classify: Classifies in 3D using Frealign. Frealign employs

• pytom_scipion - autofocus: Subtomogram averaging using pytom autofocus

• pytom_scipion - frm 3d align: Subtomogram averaging using pytom autofocus

• relion - 3D auto-refine: Refines a 3D map using Relion. Relion employs an empirical

• relion - 3D classification: Classifies in 3D using Relion. Relion employs an empirical

• relion - post-processing: Reconstructs a volume using Relion from a given set of particles

• relion - reconstruct: Reconstructs a volume using Relion from a given set of particles

• resmap - local resolution: Computes the local resolution of 3D reconstructions

• simple - prime: Produces one or several initial volumes using simple prime

• spider - reconstruct fourier: Simple reconstruction protocol using Fourier back projection

• spider - refinement: Iterative reference-based refinement of orientations

• xmipp3 - align volume: Aligns a set of volumes using cross correlation

• xmipp3 - align volume web: Aligns a set of volumes using cross correlation

• xmipp3 - apply 3d mask: Applies mask to a volume

• xmipp3 - calculate strain: Compares two states of a volume to analyze the local strains and rotations

• xmipp3 - calculator3D: Applies an operation to two sets of volumes

• xmipp3 - cltomo: Averages a set of subtomograms taking into account the missing edge

• xmipp3 - compare reprojections: Compares a set of classes or averages with the corresponding projections of a reference volume

• xmipp3 - convert a PDB: Converts a PDB file to a volume.

• xmipp3 - convert to pseudoatoms: Converts an EM volume into pseudoatoms

• xmipp3 - create 3d mask: Creates a 3D mask

• xmipp3 - crop/resize volumes: Crops or resizes a set of volumes

• xmipp3 - filter volumes: Applies Fourier filters to a set of volumes

• xmipp3 - helical symmetry: Estimates helical parameters and symmetrizes

• xmipp3 - highres: 3D refinement protocol whose main input is a volume and a set of particles

• xmipp3 - multireference_aligneability: Reconstructs a volume using Xmipp_reconstruct_fourier from a given set of particles

• xmipp3 - nma alignment: Flexible angular alignment

• xmipp3 - nma dimred: Takes the images with NMA deformations

• xmipp3 - preprocess volumes: Xmipp-based volume preprocessing

• xmipp3 - projection matching: 3D reconstruction and classification using multireference projection matching

• xmipp3 - random conical tilt: Creates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm

• xmipp3 - ransac: Computes an initial 3d model from a set of projections/classes

• xmipp3 - reconstruct fourier: Reconstructs a volume using Xmipp_reconstruct_fourier from a given set of particles

• xmipp3 - reconstruct significant: Addresses the initial volume problem in SPA

• xmipp3 - resolution 3D: Computes resolution by several methods

• xmipp3 - split volume: Splits volume in two

• xmipp3 - validate tilt: Validates initial volumes by using a set of projections/classes from a tilted-pair picking process and using a RCT algorithm

• xmipp3 - validate_nontilt: Ranks a set of volumes according to their alignment reliability obtained from a clusterability test

By Packages

xmipp3 (58 protocols)

• xmipp3 - align volume: Aligns a set of volumes using cross correlation

• xmipp3 - align volume web: Aligns a set of volumes using cross correlation

• xmipp3 - align with cl2d: Aligns a set of particles using the CL2D algorithm

• xmipp3 - apply 2d mask: Applies a mask to a set of particles

• xmipp3 - apply 3d mask: Applies a mask to a volume

• xmipp3 - apply alignment 2d: Applies alignment parameters and produces a new set of images

• xmipp3 - assignment tiltpair: From two sets of points (tilted and untilted) the protocol determines the affine transformation between

• xmipp3 - auto-picking (step 2): Picks particles automatically in a set of micrographs using previous training

• xmipp3 - break symmetry: Classifies particles according their similarity to others in order to detect outliers

• xmipp3 - calculate strain: Compares two states of a volume to analyze the local strains and rotations

• xmipp3 - calculator2D: Applies an operation to two sets of particles

• xmipp3 - calculator3D: Applies an operation to two sets of volumes

• xmipp3 - cl2d: Classifies a set of images using a clustering algorithm

• xmipp3 - cltomo: Averages a set of subtomograms taking into account the missing edge

• xmipp3 - compare reprojections: Compares a set of classes or averages with the corresponding projections of a reference volume

• xmipp3 - consensus picking: Estimates the agreement between different particle picking algorithms. The protocol

• xmipp3 - convert a PDB: Converts a PDB file to a volume

• xmipp3 - convert to pseudoatoms: Converts an EM volume into pseudoatoms

• xmipp3 - create 2d mask: Creates a 2D mask

• xmipp3 - create 3d mask: Creates a 3D mask

• xmipp3 - crop/resize particles: Crops or resizes a set of particles

• xmipp3 - crop/resize volumes: Crops or resizes a set of volumes

• xmipp3 - ctf discrepancy: Estimates the agreement between different estimations of the CTF

• xmipp3 - ctf estimation: Estimates CTF on a set of micrographs using Xmipp 3.1

• xmipp3 - ctf_correct_wiener2d: Performs CTF correction by Wiener filtering

• xmipp3 - denoise particles: Removes particles noise by filtering them. This filtering process is based on a projection over a basis created from some averages (extracted from classes). This filtering is not intended for processing particles. The huge filtering they will be passed through is known to remove part of the signal

• xmipp3 - extract particle pairs: Extracts particles from a set of tilted pairs' coordinates

• xmipp3 - extract particles: Extracts particles from a set of coordinates

• xmipp3 - filter particles: Applies Fourier filters to a set of particles

• xmipp3 - filter volumes: Applies Fourier filters to a set of volumes

• xmipp3 - helical symmetry: Estimates helical parameters and symmetrize.

• xmipp3 - highres: 3D refinement protocol whose main input is a volume and a set of particles.

• xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM)

• xmipp3 - manual-picking (step 1): Picks particles in a set of micrographs using Xmipp

• xmipp3 - ml2d: Performs (multi-reference) 2D alignment using

• xmipp3 - movie alignment: Aligns movies, from direct detectors cameras, into micrographs

• xmipp3 - movie extract particles: Extracts a set of particles from each frame of a set of movies

• xmipp3 - multireference_aligneability: Reconstructs a volume using Xmipp_reconstruct_fourier from a given set of particles

• xmipp3 - nma alignment: Flexible angular alignment.

• xmipp3 - nma analysis: Flexible angular alignment using normal modes

• xmipp3 - nma cluster: Protocol executed when a cluster is created

• xmipp3 - nma dimred: This protocol will take the images with NMA deformations

• xmipp3 - preprocess micrographs: Preprocesses a set of micrographs in the project. Can crop borders, remove bad pixels, etc.

• xmipp3 - preprocess particles: Preprocesses a set of particles. Can remove dust, normalize, apply threshold, etc

• xmipp3 - preprocess volumes: Xmipp-based volume preprocessing

• xmipp3 - projection matching: 3D reconstruction and classification using multireference projection matching

• xmipp3 - random conical tilt: Creates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm

• xmipp3 - ransac: Computes an initial 3D model from a set of projections/classes

• xmipp3 - reconstruct fourier: Reconstructs a volume using Xmipp_reconstruct_fourier from a given set of particles

• xmipp3 - reconstruct significant: Addresses the initial volume problem in SPA

• xmipp3 - resolution 3D: Computes resolution by several methods

• xmipp3 - rotational spectra: Computes the rotational spectrum of the given particles

• xmipp3 - screen classes: Compares a set of classes or averages with the corresponding projections of a reference volume

• xmipp3 - screen particles: Classifies particles according their similarity to the others in order to detect outliers

• xmipp3 - split volume: Splits volume in two

• xmipp3 - tilt pairs particle picking: Picks particles in a set of micrographs using Xmipp

• xmipp3 - validate tilt: Validates initial volumes by using a set of projections/classes from a tilted-pair picking process and using RCT algorithm

• xmipp3 - validate_nontilt: Ranks a set of volumes according to their alignment reliability obtained from a clusterability test

scipion (20 protocols)

• scipion - alignment assign: Assigns the alignment calculated for a set of particles to another set

• scipion - classes consensus: Compares two SetOfClasses

• scipion - create mask:

• scipion - create subset: Creates subsets from the GUI

• scipion - ctf assign: Assigns a CTF estimation to a particular

• scipion - extract coordinates: Extracts the coordinates information from a set of particles

• scipion - import averages: Imports a set of averages to the project

• scipion - import coordinates: Imports a set of coordinates

• scipion - import ctf: Imports a set of CTFs into the project

• scipion - import mask: Class to import masks from existing files

• scipion - import micrographs: Imports a set of micrographs to the project

• scipion - import movies: Imports a set of movies (from direct detector cameras) to the project

• scipion - import particles: Imports a set of particles to the project

• scipion - import pdb volumes: Imports a set of PDB volumes to the project

• scipion - import tilted micrographs: Imports untilted-tilted pairs of micrographs in the project

• scipion - import volumes: Imports a set of volumes to the project

• scipion - parallel test: A parallel test protocol.

• scipion - split sets: Splits a set into two or more subsets.

• scipion - subset: Creates a set with the elements of an original set that are also

• scipion - union sets: Joins two or more sets of images.

spider (10 protocols)

• spider - align apsr: Reference-free alignment shift and rotational alignment of an image series

• spider - align pairwise: Reference-free alignment shift and rotational alignment of an image series

• spider - capca: Correspondence Analysis (CA) or Principal Component Analysis (PCA)

• spider - classify diday: Diday’s method, using 'CL CLA'

• spider - classify kmeans: Diday’s method, using 'CL CLA'

• spider - classify ward: Ward’s method, using 'CL HC'

• spider - custom mask: Creates a custom mask

• spider - filter particles: Applies Fourier filters to an image or volume

• spider - reconstruct fourier: Simple reconstruction protocol using Fourier back projection

• spider - refinement: Iterative reference-based refinement of orientations

relion (9 protocols)

• relion - 2D classification: Wrapper around Relion 2D - class averages program

• relion - 3D auto-refine: Refines a 3D map using Relion. Relion employs an empirical

• relion - 3D classification: Classifies in 3D using Relion. Relion employs an empirical

• relion - auto-picking (step 1): Uses 2D class averages as templates to run the auto-picking using Relion

• relion - auto-picking (step 2): Uses 2D class averages as templates to run the auto-picking using Relion

• relion - particle polishing: Reconstructs a volume using Relion from a given set of particles

• relion - post-processing: Reconstructs a volume using Relion from a given set of particles

• relion - preprocess particles: Wrapper around the Relion preprocess program

• relion - reconstruct: Reconstructs a volume using Relion from a given set of particles

eman2 (5 protocols)

• eman2 - boxer: Picks particles in a set of micrographs using eman

• eman2 - initial model: Wrapper around e2initialmodel.py Eman2 program which

• eman2 - reconstruct: Wrapper around e2make3d.py Eman2 program

• eman2 - refine easy: Wrapper around e2refine_easy.py Eman2 program

• eman2 - sparx gaussian picker: Picks particles automatically in a set of micrographs using Sparx gaussian picker

grigoriefflab (5 protocols)

• grigoriefflab - Summovie: Aligns the frames of movies recorded

• grigoriefflab - Unblur: Aligns the frames of movies recorded

• grigoriefflab - ctffind: Estimates the CTF on a set of micrographs

• grigoriefflab - frealign: Refines a 3D map using Frealign. The algorithms implemented

• grigoriefflab - frealign classify: Classifies in 3D using Frealign. Frealign employs

pytom_scipion (3 protocols)

• pytom_scipion - autofocus: Subtomogram averaging using pytom autofocus

• pytom_scipion - frm 3d align: Subtomogram averaging using pytom autofocus

• pytom_scipion - import: Imports a particle list of subtomograms

bsoft (2 protocols)

• bsoft - bfilter: Wrapper around bfilter program

• bsoft - particle picking: Picks particles in a set of micrographs using bsoft

appion (1 protocols)

• appion - dogpicker: Picks particles in a set of micrographs using Appion dogpicker

emxlib (1 protocols)

• emxlib - emx export: Exports micrographs, coordinates, or particles to EMX format

resmap (1 protocols)

• resmap - local resolution: Computes the local resolution of 3D reconstructions

simple (1 protocols)

• simple - prime: Produces one or several initial volumes using SIMPLE Prime

igbmc (1 protocols)

• igbmc - auto-picking: gEMpicker is a template-based cryo-EM particle picking program that uses

cryoem_scipion (1 protocols)

• cryoem_scipion - pseudoatoms: Produces one or several initial volumes using cryoem pseudoatoms

atsas (1 protocols)

• atsas - convert PDB to SAXS curve: Protocol for converting a PDB file (true atoms or pseudoatoms) into a SAXS curve

Scipion v1.0.0 (15 Jan 2016)

>>>>> python /home/josem/work/development/workspace/scipion/pyworkflow/apps/pw_protocol_list.py "--with-doc" "--asciidoc"