COMPUTER GRAPHICS & IMAGE PROCESSING SOFTWARE FOR MOLECULAR MICROSCOPY

电脑图像

• 批准号: 6220661
• 负责人: GINA SOSINSKY
• 金额: $ 4.81万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-05-15 至 2000-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6220661
• 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的主要活动重点包括 促进对细胞结构和功能的研究 通过光学和电子显微镜的协同应用 技术，NCMIR的使命之一是提供一个地区性的资源 对于分子显微镜专家来说也是如此。为了服务于这些 调查人员，我们已经安装了分子显微镜软件。 以前安装的用于分子显微镜的软件包 包括MRC 2D晶体分析包ICE、SPECTRUM、 CCP4、SUPRIM和PHOELIX。现在和将来都会维护这些包 并进行了更新。在过去的一年里，我们调查了各种 用于装配独立结构的程序或程序套件 通过具有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射线结晶学)。 NCMIR的一个长期目标是开发或应用 整合从结构生物学获得的数据的程序 技术(分子显微镜、共聚焦显微镜、EM断层扫描、 X射线结晶学)。我们用缝隙连接尝试过的程序 EM数据包括：Xtalview、O、神经编辑器和Ducky。在……里面 特别是，我们发现Xtalview，一个为X射线开发的包 晶体分析，适合独立间隙的拟合需要 连接数据集(见Perkins等人，J.Mol.比奥尔。272,1998)。 为此，拉蒙特先生编写了一个程序来转换SYNU 将表面表示(我们的可视化软件)转化为蛋白质 数据库坐标(PDB文件)以及一个程序，该程序随后获取 修改的PDB文件，并将其转换回SYNU表示法。这些 然后，伪PDB文件可以输入到显示以下内容的任何程序 蛋白质坐标(Xtalview，O，Rasmol)。我们还试着使用 Xtalview以适应共焦和EM层析数据集。这招奏效了 只取得了有限的成功。在接下来的一年，我们还将调查AVS， 它可能比目前的X射线具有更大的灵活性 结晶学软件，作为一个拟合和可视化环境。 与圣地亚哥超级计算机中心(SDSC)和 由国家科学基金会提供的补充支持，索辛斯基博士 创建了EM外联计划。这项计划的目标是 两重。第一，将NCMIR开发为软件环境，并 为研究提供工具和专业知识的资源；第二，提供 基于Web的教育材料和研究工具 技术。为了利用国家的优势 SDSC为我们提供的基础设施，EM外联计划是 位于SDSC网站上。EM外展计划位于 网址：em-outreach.sdsc.edu.EM外展计划包括(1) 有关EM软件应用程序的网页形式的信息或 文档和(2)包含文本和图表的课程 电子显微镜结构分析的Web文档格式 (网络课程的原始素材来自Tim博士 贝克，普渡大学)。EM外展计划哈S 在1997年戈登三维显微镜会议上做的广告 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 以及对当前教育网站中的文字和图形进行修改 页面，在文本中创建向上/向下链接，合并搜索 主题引擎(索引)、指向相应参考文献的链接、指向 图像处理部分中的相应软件，提供教程链接 关于如何使用软件和实现任何动画和/或高级 网络技术。