2008Scheres XmippProtocols

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S. H. W. Scheres, R. Núñez-Ramírez, C.O.S. Sorzano, J.M. Carazo, R. Marabini. Image processing for electron microscopy single-particle analysis using Xmipp. Nature protocols, 3: 977-990 (2008)

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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.


Image processing protocols, single particles


Article http://www.ncbi.nlm.nih.gov/pubmed/18536645

Related software

Xmipp: http://xmipp.cnb.csic.es

Related methods