https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2008Scheres_XmippProtocols 2026-05-24T19:51:41Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2008Scheres_XmippProtocols&diff=1510&oldid=prev 2009-04-02T11:54:40Z

<p></p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> 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)<br /> <br /> [http://scholar.google.com/scholar?hl=en&amp;lr=&amp;newwindow=1&amp;cites=6895666067902788644 Cited by]<br /> <br /> == Abstract ==<br /> <br /> 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.<br /> <br /> == Keywords ==<br /> <br /> Image processing protocols, single particles<br /> <br /> == Links ==<br /> <br /> Article http://www.ncbi.nlm.nih.gov/pubmed/18536645<br /> <br /> == Related software ==<br /> <br /> Xmipp: http://xmipp.cnb.csic.es<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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