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: Import a particle list of subtomograms

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

• scipion - import coordinates: Protocol to import a set of coordinates

• scipion - import ctf: Common protocol to import a set of ctfs into the project

• scipion - import mask: Class for import masks from existing files.

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

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

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

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

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

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

Micrographs

• grigoriefflab - Summovie: Summovie is used to align the frames of movies recorded

• grigoriefflab - Unblur: Unblur is used to align the frames of movies recorded

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

• scipion - ctf assign: This protocol assign a CTF estimation to a particular

• xmipp3 - ctf discrepancy: Protocol to estimate the agreement between different estimation of the CTF

• xmipp3 - ctf estimation: Protocol to estimate 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: Extract a set of Particles from each frame of a set of Movies.

• xmipp3 - preprocess micrographs: Protocol to preprocess a set of micrographs in the project. You can crop borders, remove bad pixels, etc.

Particles

• appion - dogpicker: Protocol to pick particles in a set of micrographs using appion dogpicker

• bsoft - bfilter: Wrapper around bfilter program.

• bsoft - particle picking: Protocol to pick particles in a set of micrographs using bsoft

• eman2 - boxer: Protocol to pick particles in a set of micrographs using eman

• eman2 - sparx gaussian picker: Protocol to pick 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 use

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

• relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking

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

• relion - preprocess particles: Wrapper to Relion preprocess program.

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

• scipion - import coordinates: Protocol to import a set of coordinates

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

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

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

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

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

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

• xmipp3 - consensus picking: Protocol to estimate the agreement between different particle picking algorithms. The protocol

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

• xmipp3 - ctf_correct_wiener2d: Perform CTF correction by Wiener filtering.

• xmipp3 - denoise particles: Remove 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: Protocol to extract particles from a set of tilted pairs coordinates

• xmipp3 - extract particles: Protocol to extract particles from a set of coordinates

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

• xmipp3 - manual-picking (step 1): Xmipp protocol to pick particles in a set of micrographs

• xmipp3 - movie extract particles: Extract a set of Particles from each frame of a set of Movies.

• xmipp3 - preprocess particles: Preprocess a set of particles. You can remove dust, normalize, apply threshold, etc

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

• xmipp3 - tilt pairs particle picking: Xmipp protocol to pick particles in a set of micrographs

2D

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

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

• scipion - classes consensus: Compare 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: This step creates a custom mask.

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

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

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

• xmipp3 - create 2d mask: Create a 2D mask.

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

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

• xmipp3 - rotational spectra: Protocol to compute 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: Protocol for converting 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: This Protocol wraps e2initialmodel.py Eman2 program which

• eman2 - reconstruct: This Protocol wraps e2make3d.py Eman2 program.

• eman2 - refine easy: This Protocol wraps e2refine_easy.py Eman2 program.

• grigoriefflab - frealign: Protocol to refine a 3D map using Frealign. The algorithms implemented

• grigoriefflab - frealign classify: Protocol to classify 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: Protocol to refine a 3D map using Relion. Relion employs an empirical

• relion - 3D classification: Protocol to classify 3D using Relion. Relion employs an empirical

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

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

• resmap - local resolution: ResMap is software tool for computing the local resolution of 3D

• 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: Apply mask to a volume

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

• xmipp3 - calculator3D: Apply 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: Covert a PDB file to a volume.

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

• xmipp3 - create 3d mask: Create a 3D mask.

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

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

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

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

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

• xmipp3 - nma alignment: Protocol for flexible angular alignment.

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

• xmipp3 - preprocess volumes: Protocol for Xmipp-based preprocess for volumes

• 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: Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles.

• xmipp3 - reconstruct significant: This algorithm addresses the initial volume problem in SPA

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

• xmipp3 - split volume: Split volume in two

• 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.

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: Apply mask to a set of particles

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

• xmipp3 - apply alignment 2d: Apply 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

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

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

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

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

• xmipp3 - calculator3D: Apply 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: Protocol to estimate the agreement between different particle picking algorithms. The protocol

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

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

• xmipp3 - create 2d mask: Create a 2D mask.

• xmipp3 - create 3d mask: Create a 3D mask.

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

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

• xmipp3 - ctf discrepancy: Protocol to estimate the agreement between different estimation of the CTF

• xmipp3 - ctf estimation: Protocol to estimate CTF on a set of micrographs using Xmipp 3.1

• xmipp3 - ctf_correct_wiener2d: Perform CTF correction by Wiener filtering.

• xmipp3 - denoise particles: Remove 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: Protocol to extract particles from a set of tilted pairs coordinates

• xmipp3 - extract particles: Protocol to extract particles from a set of coordinates

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

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

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

• xmipp3 - highres: This is a 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): Xmipp protocol to pick particles in a set of micrographs

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

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

• xmipp3 - movie extract particles: Extract a set of Particles from each frame of a set of Movies.

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

• xmipp3 - nma alignment: Protocol for 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: Protocol to preprocess a set of micrographs in the project. You can crop borders, remove bad pixels, etc.

• xmipp3 - preprocess particles: Preprocess a set of particles. You can remove dust, normalize, apply threshold, etc

• xmipp3 - preprocess volumes: Protocol for Xmipp-based preprocess for volumes

• 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: Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles.

• xmipp3 - reconstruct significant: This algorithm addresses the initial volume problem in SPA

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

• xmipp3 - rotational spectra: Protocol to compute 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: Classify particles according their similarity to the others in order to detect outliers.

• xmipp3 - split volume: Split volume in two

• xmipp3 - tilt pairs particle picking: Xmipp protocol to pick particles in a set of micrographs

• 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: Assign a the alignment calculated for a set of particles to another set.

• scipion - classes consensus: Compare two SetOfClasses

• scipion - create mask:

• scipion - create subset: Create subsets from the GUI.

• scipion - ctf assign: This protocol assign a CTF estimation to a particular

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

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

• scipion - import coordinates: Protocol to import a set of coordinates

• scipion - import ctf: Common protocol to import a set of ctfs into the project

• scipion - import mask: Class for import masks from existing files.

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

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

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

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

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

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

• scipion - parallel test: A parallel test protocol.

• scipion - split sets: Protocol to split a set in two or more subsets.

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

• scipion - union sets: Protocol to join 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: This step creates a custom mask.

• spider - filter particles: Apply 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 to Relion 2D - class averages program.

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

• relion - 3D classification: Protocol to classify 3D using Relion. Relion employs an empirical

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

• relion - auto-picking (step 2): This Relion protocol uses 2D class averages as templates to run the auto-picking

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

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

• relion - preprocess particles: Wrapper to Relion preprocess program.

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

eman2 (5 protocols)

• eman2 - boxer: Protocol to pick particles in a set of micrographs using eman

• eman2 - initial model: This Protocol wraps e2initialmodel.py Eman2 program which

• eman2 - reconstruct: This Protocol wraps e2make3d.py Eman2 program.

• eman2 - refine easy: This Protocol wraps e2refine_easy.py Eman2 program.

• eman2 - sparx gaussian picker: Protocol to pick particles automatically in a set of micrographs using sparx gaussian picker

grigoriefflab (5 protocols)

• grigoriefflab - Summovie: Summovie is used to align the frames of movies recorded

• grigoriefflab - Unblur: Unblur is used to align the frames of movies recorded

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

• grigoriefflab - frealign: Protocol to refine a 3D map using Frealign. The algorithms implemented

• grigoriefflab - frealign classify: Protocol to classify 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: Import a particle list of subtomograms

bsoft (2 protocols)

• bsoft - bfilter: Wrapper around bfilter program.

• bsoft - particle picking: Protocol to pick particles in a set of micrographs using bsoft

appion (1 protocols)

• appion - dogpicker: Protocol to pick particles in a set of micrographs using appion dogpicker

emxlib (1 protocols)

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

resmap (1 protocols)

• resmap - local resolution: ResMap is software tool for computing the local resolution of 3D

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 use

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"