The EMXtalOrg suite was written to provide a user-friendly interface to the electron microscopy (EM) 3-D merging program origtilt, which was written in user-unfriendly Fortran. It also serves to provide functions in the processing of crystalline EM image data after indexing and correction for the contrast transfer (CTF) effect. The current version uses amplitudes-and-phases (aph) data files from indexed, tilted EM images of two-dimensional (2D) protein crystals, such as those output by the SPECTRA indexing program included with the Integrated Crystallographic Environment (I.C.E.) suite ( http://ncmi.bcm.tmc.edu/software/software.html). After merging the files in tilt_org and processing with aph_edit, a standard HKL-type file or several program-specific file-types can be output which can be used as input to a number of 3-D image processing and visualization programs including CCP4 (http:// www.dl.ac.uk/CCP/CCP4/main.html) and XtalView (http://www.scripps.edu/pub/dem-web/).