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Nat Protoc. 2008;3(6):977-90. doi: 10.1038/nprot.2008.62.

Image processing for electron microscopy single-particle analysis using XMIPP.

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1
Centro Nacional de Biotecnología CSIC, Unidad de Biocomputación, Cantoblanco, 28049 Madrid, Spain.

Abstract

We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.

PMID:
18536645
PMCID:
PMC2778070
DOI:
10.1038/nprot.2008.62
[Indexed for MEDLINE]
Free PMC Article
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