COMPUTER GRAPHICS & IMAGE PROCESSING SOFTWARE FOR MOLECULAR MICROSCOPY

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While the major focus of activity at the NCMIR involves facilitation of investigations into cellular structure and function through coordinated application of light and electron microscopy techniques, part of NCMIR's mission is to provide a regional resource for molecular microscopists as well. In order to service these investigators, we have set up software for molecular microscopy. Packages for molecular microscopy that were previously installed include the MRC 2D crystallographic analysis package, ICE, SPECTRA, CCP4, SUPRIM and PHOELIX. These packages are and will be maintained and updated. During the past year, we have investigated various programs or suite of programs for fitting of independent structures obtained by structural techniques with differing levels of resolution (e.g. electron microscopy, light microscopy, X-ray crystallography). A long-term goal of NCMIR is the development or application of programs for integrating data obtained from structural biology techniques (molecular microscopy, confocal microscopy, EM tomography, X-ray crystallography). Programs we have tried with the gap junction EM data include: Xtalview, O, Neural Editor and Ducky. In particular, we found that Xtalview, a package developed for X-ray crystallographic analysis, suited the needs of fitting independent gap junction data sets (see Perkins et al., J. Mol. Biol. 272, 1998). For this purpose, Mr. Lamont wrote a program for converting the SYNU surface representations (our visualization software) into protein database coordinates (PDB files) as well as a program that then takes modified pdb file and converts it back to SYNU representations. These pseudo-PDB files can then inputed into any programs that display protein coordinates (Xtalview, O, Rasmol). We also tried using Xtalview to fit a confocal and EM tomographic data set. This worked with limited success. In the next year, we will also investigate AVS, which may have more flexibility than the current X-ray crystallographic software, as a fitting and visualization environment. In conjunction with the San Diego Supercomputer Center (SDSC) and with supplemental support by the National Science Foundation, Dr. Sosinsky created the EM Outreach Program. The goals of this program are twofold. First, to develop NCMIR as a software environment and resource for tools and expertise for research and second, to provide educational materials as well as research tools via web based technologies. In order to take advantage of the national infrastructure afforded to us by SDSC, the EM Outreach program is located on an SDSC Web Site. The EM Outreach program is found at the URL: em-outreach.sdsc.edu.. The EM Outreach program contains (1) information in the form of Web pages about EM software applications or documentation and (2) a course complete with text and figures in the form of Web documents on structure analysis for electron microscopy (original source material for the web course was obtained from Dr. Tim Baker, Purdue University). The EM Outreach program ha s been advertised at the 1997 Gordon Conference on 3D Microscopy, Microscopy Society of America 1997 meeting and the 1997 Neuroscience meeting. Our plans for the coming year include expanding the software pages as well as revising the text and figures in current educational web pages, creating up/down Links within texts, incorporating a search engine for topics (index), links to appropriate references, links to appropriate software in image processing section, links to tutorials on how to use software and implementing any animations and/or advanced web technology.