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Protocols

Scipion specifications

Information


Unique identifier OMICS_14119
Name Scipion
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Input data Some CTF, coordinates, micrographs or particles.
Input format CTFPARAM, LOG, TXT, OUT, LOG, BOX, JSON, POS, STAR, EMX, SCIPION, XMIPP
Output data The 3D models of macromolecular complexes.
Operating system Unix/Linux
Programming languages C++, Java, Javascript, Python
License GNU General Public License version 3.0
Computer skills Medium
Version 1.2.1
Stability Stable
Requirements
OpenJDK, libopenmpi-dev, openmpi-bin, gfortran
Maintained Yes

Subtool


  • LocalDeblur

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Jose Miguel de la Rosa-Trevín

Additional information


https://github.com/I2PC/scipion/wiki

Information


Unique identifier OMICS_14119
Name Scipion
Interface Web user interface
Restrictions to use None
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • LocalDeblur

Documentation


Maintainer


  • person_outline Jose Miguel de la Rosa-Trevín

Additional information


https://github.com/I2PC/scipion/wiki

Publications for Scipion

Scipion citations

 (18)
call_split

Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins

2018
PLoS Pathog
PMCID: 5823459
PMID: 29470533
DOI: 10.1371/journal.ppat.1006837
call_split See protocol

[…] ith pixel size of 2.18A and defocus of 1.2–1.8 μm. The tilt pair was collected at -60° and 0°.To generated 3D model of the RSV F-Fab complexes we used the RCT approach. Data processing was done using Scipion suit []. First tilt-pairs from the micrographs were picked using xmipp3—tilt pairs particle picking [,] with box size of 160 x 160 pixels. The particles were extract and binned by 2 to generat […]

call_split

The structure of an elongation factor G ribosome complex captured in the absence of inhibitors

2018
Nucleic Acids Res
PMCID: 5887593
PMID: 29408956
DOI: 10.1093/nar/gky081
call_split See protocol

[…] s were acquired in movie mode at 7 frames per exposure (1 s). The original image stacks were corrected for drift and beam-induced motion and summed using the optical flow approach () accessed through Scipion (). The contrast transfer function parameters and defocus values for each micrograph were determined using CTFFIND 4 (). EMAN2 () e2boxer software was used for semi-automatic particle picking, […]

call_split

Cryo‐EM reconstruction of Type VI secretion system baseplate and sheath distal end

2017
PMCID: 5813253
PMID: 29255010
DOI: 10.15252/embj.201797103
call_split See protocol

[…] on for each micrograph was estimated using CTFFIND4 (Rohou & Grigorieff, ). 2,248 particles corresponding to the ends of extended T6SS assemblies were picked using XMIPP manual picking utility within SCIPION framework (de la Rosa‐Trevín et al, ). Extracted particles were phase‐flipped and subjected for reference‐free 2D classification without CTF correction in RELION1.4 (Scheres, ). […]

library_books

Nucleotide– and Mal3 dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics

2017
Nat Commun
PMCID: 5727398
PMID: 29235477
DOI: 10.1038/s41467-017-02241-5

[…] in total 994 movies with a total dose of 30 e−/Å2 fractioned into 50 frames at a pixel size of 1.39 Å/px. Initial frame alignment was done with IMOD. A second local alignment step was performed with Scipion using the optical flow method. In the final reconstruction, only frames 2–21 were included resulting in a total dose of 12 e−/Å2. […]

library_books

Cryo EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h

2017
PMCID: 5668856
PMID: 29123673
DOI: 10.1107/S205225251701226X

[…] ni et al., 2017), performing image-processing tasks while new data are being acquired at the microscope (Focus; Biyani et al., 2017), incorporating different image processing into a single framework (Scipion; de la Rosa-Trevín et al., 2016) and using a pipeline approach (Fernandez-Leiro & Scheres, 2017) will further improve the integration of experimental and computational parts of cryo-EM into a […]

call_split

Pea PSII LHCII supercomplexes form pairs by making connections across the stromal gap

2017
Sci Rep
PMCID: 5577252
PMID: 28855679
DOI: 10.1038/s41598-017-10700-8
call_split See protocol

[…] ing the image frames with in-house developed software (https://github.com/dtegunov/k2align). Aligned images were used for single particle analysis. All image processing steps were performed using the Scipion platform (http://scipion.cnb.csic.es), which is an image processing framework that integrates several software packages into a unified interface. For estimating the objective lens defocus para […]

Citations

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Scipion institution(s)
Centro Nacional de Biotecnologıa (CNB-CSIC), Cantoblanco, Madrid, Spain
Scipion funding source(s)
Supported by the Spanish Ministry of Economy and Competitiveness through grants AIC-A011-0638 and BIO2016-76400-R, Fundacion General CSIC (Programa ComFuturo), the European Union (EU), the Horizon 2020 through grants: EINFRA2014-2: EGI Engage (Proposal: 654142) and EINFRA-2015-1:West-Life (Proposal: 675858) and NVIDIA.

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