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Xmipp specifications


Unique identifier OMICS_15598
Name Xmipp
Alternative name X-Window-based Microscopy Image Processing Package
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java, Python, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Medium
Version 3.1
Stability Stable
Maintained No




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Publications for X-Window-based Microscopy Image Processing Package

Xmipp citations


Cryo EM of nucleosome core particle interactions in trans

Sci Rep
PMCID: 5935684
PMID: 29728587
DOI: 10.1038/s41598-018-25429-1
call_split See protocol

[…] with the Unblur software package with a dose filter. We collected ~2000 micrographs from several independent NCP preparations. Several thousand particles were manually picked and carefully cleaned in XMIPP to remove inconsistent particles. The resulting useful particles were then used for semi-automatic and automatic particle picking in XMIPP. The contrast transfer function parameters were determi […]


Structure and mechanism of the two component α helical pore forming toxin YaxAB

Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] fication on a Tecnai Spirit (FEI) operated at 120 kV using either Eagle 4 K (FEI) or TVIPS F416 detectors (Tietz Camera Systems). Automated particle picking and 2D classification were performed using Xmipp 3.0. Based on the 2D averages, 14,600 particles were selected and imported into RELION. Using IMAGIC the initial model for the negative stain 3D reconstruction was generated from three 2D averag […]


Mutations in VP1 and 5′ UTR affect enterovirus 71 virulence

Sci Rep
PMCID: 5923339
PMID: 29703921
DOI: 10.1038/s41598-018-25091-7
call_split See protocol

[…] × 4 k CCD Camera System (Model 895). Virions harvested from RD and Vero cells were selected manually using the e2boxer.py package in EMAN2. ML2D, an image classification algorithm package included in Xmipp 3.1, was used to classify the selected particles as empty or full. The crystal structure of the EV-VP1 protein (PDB ID code: 3VBS) was manually fitted into the mature EV71 cryoEM structure (EMDB […]


Structural rearrangements of the histone octamer translocate DNA

Nat Commun
PMCID: 5889399
PMID: 29626188
DOI: 10.1038/s41467-018-03677-z
call_split See protocol

[…] th a total exposure of 100 e Å−2. Forty frames were collected and aligned with the Unblur software package using a dose filter.Several thousand particles were manually picked and carefully cleaned in XMIPP to remove inconsistent particles. The resulting useful particles were used for semi-automatic and automatic particle picking in XMIPP. The contrast transfer function parameters were determined u […]


Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins

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

[…] ected 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 generate a box size of 80 x 80 pixels (4.36 A/px). The images were normalized us […]


Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase

PLoS Pathog
PMCID: 5823471
PMID: 29425244
DOI: 10.1371/journal.ppat.1006889
call_split See protocol

[…] ed using ctffind4 []. Individual particles in the 67,000× images were selected using automated picking protocols followed by several rounds of reference-free alignment and classification based on the XMIPP processing package to sort them into self-similar groups []. […]

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Xmipp funding source(s)
This work was supported by the Comunidad de Madrid through grant CAM (S2010/BMD- 2305), the NSF through Grant 1114901, the Spanish Ministry of Economy and Competitiveness through Grants AIC-A-2011-0638 and BIO2010-16566, ‘‘Juan de la Cierva’’ postdoctoral grants with references JCI-2011-10185 and JCI-2010- 07594, and predoctoral grants with references BES-2011-044096 and JAEPre_09_01717, by a Ramón y Cajal fellowship, and partially by Instruct, which is part of the European Strategy Forum on Research Infrastructures (ESFRI) and supported by national member subscriptions.

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