COMPUTER GRAPHICS & IMAGE PROCESSING SOFTWARE FOR MOLECULAR MICROSCOPY

电脑图像

• 批准号: 6469022
• 负责人: GINA SOSINSKY
• 金额: $ 10.66万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-05-01 至 2002-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6469022
• 关键词: bioengineering /biomedical engineering; biomedical equipment development; biomedical resource; biotechnology; building /facility design /renovation; technology /technique

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.

虽然 NCMIR 活动的主要重点涉及 促进细胞结构和功能的研究 通过光学和电子显微镜的协调应用 技术，NCMIR 使命的一部分是提供区域资源 对于分子显微镜学家来说也是如此。 为了服务这些 研究人员，我们已经建立了分子显微镜软件。 先前安装的分子显微镜软件包 包括 MRC 2D 晶体分析包、ICE、SPECTRA、 CCP4、SUPRIM 和 PHOELIX。 这些包现在和将来都会得到维护 并更新。 在过去的一年里，我们调查了各种 用于安装独立结构的程序或程序套件 通过不同分辨率级别的结构技术获得 （例如电子显微镜、光学显微镜、X 射线晶体学）。 NCMIR的一个长期目标是开发或应用 用于整合从结构生物学获得的数据的程序 技术（分子显微镜、共焦显微镜、EM 断层扫描、 X 射线晶体学）。 我们尝试过间隙连接的程序 EM 数据包括：Xtalview、O、Neural Editor 和 Ducky。 在 特别是，我们发现 Xtalview，一个为 X 射线开发的软件包 晶体学分析，适合拟合独立间隙的需要 连接数据集（参见 Perkins 等人，J. Mol. Biol. 272， 1998）。 为此，Lamont先生编写了一个转换SYNU的程序 蛋白质的表面表征（我们的可视化软件） 数据库坐标（PDB 文件）以及随后采用的程序 修改 pdb 文件并将其转换回 SYNU 表示形式。 这些 然后可以将伪 PDB 文件输入到显示的任何程序中 蛋白质坐标（Xtalview，O，Rasmol）。 我们也尝试使用 Xtalview 用于拟合共焦和 EM 断层扫描数据集。 这有效 取得的成功有限。 明年我们还会调查AVS， 这可能比目前的 X 射线具有更大的灵活性 晶体学软件，作为拟合和可视化环境。 与圣地亚哥超级计算机中心 (SDSC) 合作并 国家科学基金会 Sosinsky 博士的补充支持 创建了 EM 外展计划。 该计划的目标是 双重。 首先，开发NCMIR作为软件环境并 第二，提供研究工具和专业知识资源 通过网络提供的教育材料和研究工具 技术。 为了利用国家 SDSC 为我们提供了基础设施，EM 外展计划是 位于 SDSC 网站上。 EM Outreach 计划位于 URL: em-outreach.sdsc.edu.. EM Outreach 计划包含 (1) 有关 EM 软件应用程序的网页形式的信息或 文档和 (2) 包含文本和图形的课程 电子显微镜结构分析的网络文档形式 （网络课程的原始资料来自 Tim 博士 贝克，普渡大学）。 新兴市场外展计划已 在 1997 年戈登 3D 显微镜会议上做广告，显微镜 美国学会1997年会议和1997年神经科学会议。 我们来年的计划包括将软件页面扩展为 以及修改当前教育网站中的文字和图表 页面、在文本中创建上/下链接、合并搜索 主题引擎（索引）、相应参考文献的链接、 图像处理部分的适当软件，教程链接 关于如何使用软件和实现任何动画和/或高级 网络技术。