00876nas a2200133 4500008004100000245005300041210005200094490000600146520041000152100001800562700001700580700001900597856012600616 2012 eng d00aUse of SPIDER and SPIRE in Image Reconstruction.0 aUse of SPIDER and SPIRE in Image Reconstruction0 vF3 aSPIDER is a comprehensive command-operated suite of programs for image processing in electron microscopy, with special emphasis on single-particle reconstruction. This chapter provides an outline of the way SPIDER and SPIRE, its interactive graphical user interface, may be used to obtain a three-dimensional reconstruction from projections of many randomly oriented realizations of a biological molecule.1 aLeith, ArDean1 aBaxter, Bill1 aFrank, Joachim uhttp://xrpp.iucr.org/cgi-bin/itr?url_ver=Z39.88-2003&rft_dat=what%3Dchapter%26volid%3DFb%26chnumo%3D19o8%26chvers%3Dv000101670nas a2200289 4500008004100000022001400041245011900055210006900174260001200243300001200255490000600267520076600273653004001039653002501079653002201104653002401126653001301150653002801163100002201191700001701213700001701230700002701247700002101274700001801295700001901313856004801332 2008 eng d a1750-279900aSPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.0 aSPIDER image processing for singleparticle reconstruction of bio c10/2008 a1941-740 v33 a

This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.

10aImage Processing, Computer-Assisted10aMicroscopy, Electron10aModels, Molecular10aMolecular Structure10aSoftware10aUser-Computer Interface1 aShaikh, Tanvir, R1 aGao, Haixiao1 aBaxter, Bill1 aAsturias, Francisco, J1 aBoisset, Nicolas1 aLeith, ArDean1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1918007801572nas a2200217 4500008004100000022001400041245004500055210004300100260001200143300001000155490000800165520098000173653002601153653004001179653001301219653002001232100001701252700001801269700001901287856004801306 2007 eng d a1047-847700aSPIRE: the SPIDER reconstruction engine.0 aSPIRE the SPIDER reconstruction engine c01/2007 a56-630 v1573 a

SPIRE is a Python program written to modernize the user interaction with SPIDER, the image processing system for electron microscopical reconstruction projects. SPIRE provides a graphical user interface (GUI) to SPIDER for executing batch files of SPIDER commands. It also lets users quickly view the status of a project by showing the last batch files that were run, as well as the data files that were generated. SPIRE handles the flexibility of the SPIDER programming environment through configuration files: XML-tagged documents that describe the batch files, directory trees, and presentation of the GUI for a given type of reconstruction project. It also provides the capability to connect to a laboratory database, for downloading parameters required by batch files at the start of a project, and uploading reconstruction results at the end of a project.

10aComputational Biology10aImage Processing, Computer-Assisted10aSoftware10aSoftware Design1 aBaxter, Bill1 aLeith, ArDean1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1705574301856nas a2200121 4500008004100000245008400041210006900125520138600194100001701580700001801597700001901615856010001634 2002 eng d00aA scripting language approach to control software for cryo-electron microscopy.0 ascripting language approach to control software for cryoelectron3 aCryo-electron microscopy (Cryo-EM) of single particles has developed into a widely used technique for determining the 3-dimensional structure of large molecules and molecular assemblies. The low signal-to-noise ratio of cryo-EM requires thousands of images of single molecules to be averaged together. The field has matured to the point where realization of high-resolution structures is limited primarily by computational constraints. These constraints are at the algorithmic level, as well as the control level, where dozens of complex procedures and thousands of mathematical operations are applied to the raw data. SPIDER is a highly modular and flexible software package for single particle reconstruction. A typical reconstruction project involves dozens of procedure files, which in turn draw on hundreds of available low-level operations. In the present system, it is virtually impossible to rerun the system from selected branching points in the process flow to determine the effects of various parameters values. A Reconstruction Engine (RE) is being developed as a high-level "shell" for controlling processes in the SPIDER software system. The RE allows backtracking, optimization of parameters, and automation of processing flow. The RE is implemented in a scripting language, Python, which provides an overall management capability at the global level of the project.1 aBaxter, Bill1 aLeith, ArDean1 aFrank, Joachim uhttp://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1029253&abstractAccess=no&userType=inst