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)
  • 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

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

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

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

• scipion - import mask: Imports masks from existing files into the project

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

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

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

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

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

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

Micrographs

• grigoriefflab - Summovie: Generates frame sums that can be used in subsequent image processing steps and optionally applies an exposure-dependent filter to maximize the signal at all resolutions in the frame averages.

• grigoriefflab - Unblur: Aligns the frames of movies recorded on direct detector cameras to reduce image blurring caused by beam-induced motion.

• grigoriefflab - ctffind: Estimates CTF on a set of micrographs using either ctffind3 or ctffind4 program.

• scipion - ctf assign: Assigns a CTF estimation to a particular set of particles, producing a new set.

• xmipp3 - ctf discrepancy: Estimates the agreement between different estimations of the CTF for the same set of micrographs.

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

• xmipp3 - movie alignment: Aligns movies, from direct detectors cameras, and sums them 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. 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 Bsoft bfilter program

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

• eman2 - boxer: Picks particles in a set of micrographs using the EMAN2 e2boxer.py program

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

• igbmc - auto-picking: gEMpicker is a GPU-driven template-based particle picking program that uses cross-correlation approach.

• relion - auto-picking (step 1): This Relion protocol uses 2D class averages as templates to run the auto-picking. In this first stage, the auto-picking will be run just in few micrographs to optimize two main parameters: Picking threshold and Minimum inter-particle distance. It will write out so-called FOM maps: two large (micrograph-sized) files per reference.

• relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking. In this second stage, the protocol reads the FOM maps to optimize the Threshold and Minimum inter-particle distance.

• relion - particle polishing: Tracks particle movement in movie frames, applies a resolution and dose-dependent weighting scheme for each frame and finally sums them together.

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

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

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

• spider - filter particles: Applies Fourier filters to an image or volume using Spider FQ or FQ NP programs.

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

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

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

• xmipp3 - break symmetry: Given an input set of particles with angular assignment, finds an equivalent angular assignment for a given symmetry. Be aware that input symmetry values follow Xmipp conventions

• 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 with the noise. However this is a good method for clearly see which particle are we going to process before it’s done.

• 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, either manually or using supervised picking support

• 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 to their similarity to others in order to detect outliers

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

2D

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

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

• scipion - classes consensus: Compares two sets of 2D classes

• spider - align apsr: Reference-free alignment (both translational and rotational) of an image series. Uses Spider AP SR command

• spider - align pairwise: Reference-free alignment (both translational and rotational) of an image series. This alignment scheme aligns a pair of images at a time and then averages them. Then, the averages of each of those pairs are aligned and averaged, and then pairs of those pairs, etc.

• spider - capca: Executes Correspondence Analysis (CA) or Principal Component Analysis (PCA) on image data using the Spider CA S program

• spider - classify diday: Performs automatic clustering using Diday’s method and Hierarchical Ascendant Classification (HAC) using Ward’s criterion on factors produced by CA or PCA. Uses the Spider CL CLA program

• spider - classify kmeans: Performs automatic K-Means clustering and classification on factors produced by CA or PCA. Uses the Spider CL KM program

• spider - classify ward: Finds clusters of images/elements in factor space (or a selected subspace) by using Diday’s method of moving centers, and applies hierarchical ascendant classification (HAC) (using Ward’s method) to the resulting cluster centers. Uses the Spider CL HC program

• spider - custom mask: Creates a custom mask using Spider

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

• 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 to subdivide the original dataset into a given number of classes

• xmipp3 - create 2d mask: Creates a 2D mask. The mask can be created with a given geometrical shape (Circle, Rectangle, Crown…​) or it can be obtained from operating on a 2D image or a previous mask.

• xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM) and Fuzzy c-means clustering technique (FCM)

• xmipp3 - ml2d: Performs a (multi-reference) 2D alignment using a maximum-likelihood target function

• 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 cryo-em pseudoatoms

• eman2 - initial model: Wrapper around the EMAN2 e2initialmodel.py program

• eman2 - reconstruct: Wrapper around the EMAN2 e2make3d.py program

• eman2 - refine easy: Wrapper around the EMAN2 e2refine_easy.py program

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

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

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

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

• relion - post-processing: Relion post-processing protocol for automated masking, overfitting estimation, MTF-correction and B-factor sharpening

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

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

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

• spider - reconstruct fourier: A simple reconstruction protocol using Fourier back projection. Uses the Spider BP 32F program

• spider - refinement: Iterative reference-based refinement of particle orientations, based on the Spider AP SHC and AP REF programs

• xmipp3 - align volume: Aligns a set of volumes using cross correlation or a Fast Fourier method

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

• xmipp3 - apply 3d mask: Applies a 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. The mask can be created with a given geometrical shape (Sphere, Box, Cylinder…​) or it can be obtained from operating on a 3D volume or a previous 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 symmetries

• xmipp3 - highres: 3D refinement protocol whose main input is a volume and a set of particles. The set of particles has to be at full size (the finer sampling rate available), but the rest of inputs (reference volume and masks) can be at any downsampling factor.

• xmipp3 - multireference_aligneability: Performs soft alignment validation of a set of particles confronting them against a given 3DEM map. This protocol produces particle alignment precision and accuracy parameters.

• xmipp3 - nma alignment: Flexible angular alignment

• xmipp3 - nma dimred: Takes the images with NMA deformations as points in a N-dimensional space (where N is the number of computed normal modes) and projects them in a reduced space (usually with less dimensions).

• 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 using RANSAC algorithm.

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

• xmipp3 - reconstruct significant: Addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures.

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

• xmipp3 - split volume: Splits a volume into two volumes

• 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 or a Fast Fourier method

• 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 of Xmipp

• 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 produce a new set of images

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

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

• xmipp3 - break symmetry: Given an input set of particles with angular assignment, finds an equivalent angular assignment for a given symmetry. Be aware that input symmetry values follow Xmipp conventions

• 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

• 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. The mask can be created with a given geometrical shape (Circle, Rectangle, Crown…​) or it can be obtained from operating on a 2D image or a previous mask.

• xmipp3 - create 3d mask: Creates a 3D mask. The mask can be created with a given geometrical shape (Sphere, Box, Cylinder…​) or it can be obtained from operating on a 3D volume or a previous 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 estimation of the CTF for the same set of micrographs.

• xmipp3 - ctf estimation: Estimates the 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 with the noise. However this is a good method for clearly see which particle are we going to process before it’s done.

• 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 symmetries.

• xmipp3 - highres: 3D refinement protocol whose main input is a volume and a set of particles. The set of particles has to be at full size (the finer sampling rate available), but the rest of inputs (reference volume and masks) can be at any downsampling factor.

• xmipp3 - kerdensom: Classifies a set of images using Kohonen’s Self-Organizing Feature Maps (SOM) and Fuzzy c-means clustering technique (FCM)

• xmipp3 - manual-picking (step 1): Picks particles in a set of micrographs using Xmipp, either manually or using supervised picking support

• xmipp3 - ml2d: Performs a (multi-reference) 2D alignment using a maximum-likelihood target function

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

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

• xmipp3 - multireference_aligneability: Performs soft alignment validation of a set of particles confronting them against a given 3DEM map. This protocol produces particle alignment precision and accuracy parameters.

• 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: Takes the images with NMA deformations as points in a N-dimensional space (where N is the number of computed normal modes) and projects them in a reduced space (usually with less dimensions).

• xmipp3 - preprocess micrographs: Preprocesses a set of micrographs. 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 using RANSAC algorithm.

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

• xmipp3 - reconstruct significant: Addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures.

• xmipp3 - resolution 3D: Computes resolution of 3D maps 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 to their similarity to the others in order to detect outliers

• xmipp3 - split volume: Splits a volume into two volumes

• xmipp3 - tilt pairs particle picking: Picks particles in a set of untilted-tilted pairs 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 a 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 sets of 2D classes

• scipion - create mask: Creates a custom mask

• scipion - create subset: Creates subsets from the GUI

• scipion - ctf assign: Assigns a CTF estimation to a particular set of particles producing a new set.

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

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

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

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

• scipion - import mask: Imports masks from existing files into the project

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

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

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

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

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

• scipion - import volumes: Imports a set of volumes into 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 referenced in another set.

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

spider (10 protocols)

• spider - align apsr: Reference-free alignment (both translational and rotational) of an image series. Uses Spider AP SR command

• spider - align pairwise: Reference-free alignment (both translational and rotational) of an image series. This alignment scheme aligns a pair of images at a time and then averages them. Then, the averages of each of those pairs are aligned and averaged, and then pairs of those pairs, etc.

• spider - capca: Executes Correspondence Analysis (CA) or Principal Component Analysis (PCA) on image data using the Spider CA S program

• spider - classify diday: Performs automatic clustering using Diday’s method and Hierarchical Ascendant Classification (HAC) using Ward’s criterion on factors produced by CA or PCA. Uses the Spider CL CLA program

• spider - classify kmeans: Performs automatic K-Means clustering and classification on factors produced by CA or PCA. Uses the Spider CL KM program

• spider - classify ward: Finds clusters of images/elements in factor space (or a selected subspace) by using Diday’s method of moving centers, and applies hierarchical ascendant classification (HAC) (using Ward’s method) to the resulting cluster centers. Uses the Spider CL HC program

• spider - custom mask: Creates a custom mask using Spider

• spider - filter particles: Applies Fourier filters to an image or volume using the Spider FQ or FQ NP programs.

• spider - reconstruct fourier: A simple reconstruction protocol using Fourier back projection. Uses the Spider BP 32F program

• spider - refinement: Iterative reference-based refinement of particle orientations, based on the Spider AP SHC and AP REF programs

relion (9 protocols)

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

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

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

• relion - auto-picking (step 1): This Relion protocol uses 2D class averages as templates to run the auto-picking. In this first stage, the auto-picking will be run just in few micrographs to optimize two main parameters: Picking threshold and Minimum inter-particle distance. It will write out so-called FOM maps: two large (micrograph-sized) files per reference.

• relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking. In this second stage, the protocol reads the FOM maps to optimize the Threshold and Minimum inter-particle distance.

• relion - particle polishing: Tracks particle movement in movie frames, applies a resolution and dose-dependent weighting scheme for each frame and finally sums them together.

• relion - post-processing: Relion post-processing protocol for automated masking, overfitting estimation, MTF-correction and B-factor sharpening

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

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

eman2 (5 protocols)

• eman2 - boxer: Picks particles in a set of micrographs using the EMAN2 e2boxer.py program

• eman2 - initial model: Wrapper around the EMAN2 e2initialmodel.py program

• eman2 - reconstruct: Wrapper around the EMAN2 e2make3d.py program

• eman2 - refine easy: Wrapper around the EMAN2 e2refine_easy.py program

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

grigoriefflab (5 protocols)

• grigoriefflab - Summovie: Generates frame sums that can be used in subsequent image processing steps and optionally applies an exposure-dependent filter to maximize the signal at all resolutions in the frame averages.

• grigoriefflab - Unblur: Aligns the frames of movies recorded on direct detector cameras to reduce image blurring caused by beam-induced motion.

• grigoriefflab - ctffind: Estimates CTF on a set of micrographs using either ctffind3 or ctffind4 program.

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

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

bsoft (2 protocols)

• bsoft - bfilter: Wrapper around the Bsoft 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 the SIMPLE prime program

igbmc (1 protocols)

• igbmc - auto-picking: gEMpicker is a GPU-driven template-based particle picking program that uses cross-correlation approach.

cryoem_scipion (1 protocols)

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

atsas (1 protocols)

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

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This list was generated with scipion protocols --with-doc --asciidoc command