COMPUTER GRAPHICS & IMAGE PROCESSING SOFTWARE FOR MOLECULAR MICROSCOPY

电脑图像

• 批准号: 6354273
• 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: 2000
• 资助国家: 美国
• 起止时间: 2000-05-01 至 2001-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6354273
• 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.

虽然国家监测机制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调应用 技术，NCMIR的使命的一部分是提供区域资源 也是分子显微镜学家的梦想。 为了服务这些 研究人员，我们已经建立了分子显微镜的软件。 以前安装的分子显微镜软件包 包括MRC 2D晶体学分析软件包、ICE、SPECTRA CCP 4、SUPRIM和PHOELIX。 这些软件包现在和将来都将得到维护 并更新。 在过去的一年里，我们调查了各种 用于独立结构的拟合的程序或程序组 通过不同分辨率的结构技术获得 (e.g.电子显微镜、光学显微镜、X射线晶体学）。 NCMR的一个长期目标是开发或应用 整合结构生物学数据的程序 技术（分子显微镜，共聚焦显微镜，EM断层扫描， X射线晶体学）。 我们尝试过的差距结的方案 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. 272，1998）。 为此，拉蒙先生编写了一个程序， 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， 修改的pdb文件，并将其转换回SYNU表示。 这些 伪PDB文件然后可以输入到任何程序， 蛋白质坐标（Xtalview、O、Rasmol）。 我们还尝试使用 Xtalview用于拟合共焦和EM断层扫描数据集。 这工作 但成功有限。 在接下来的一年里，我们还将调查AVS， 它可能比现在的X射线更灵活 晶体学软件，作为拟合和可视化环境。 圣地亚哥超级计算机中心（SDSC）和 由国家科学基金会Sosinsky博士提供的补充支持 创建了EM外展计划。 该计划的目标是 双重的 首先，将NCMR开发为软件环境， 第二，提供研究工具和专业知识的资源， 教育材料以及研究工具，通过网络 技术. 为了充分利用国家 SDSC提供给我们的基础设施，EM外展计划是 位于SDSC网站上。 EM外展计划可在 URL：em-outreach.sdsc.edu.. EM外展计划包含（1） 有关EM软件应用程序的网页形式的信息，或 文件和（2）一个过程中完成的文本和数字， 电子显微结构分析的Web文档格式 （网络课程的原始资料来自Tim博士 Baker，Purdue University）。 EM外展计划已经 在1997年的戈登会议3D显微镜，显微镜 美国学会1997年会议和1997年神经科学会议。 我们明年的计划包括扩展软件页面， 并对现有教育网站的文字和图形进行了修改 页面，在文本中创建向上/向下链接，合并搜索 主题引擎（索引），链接到适当的参考资料，链接到 图像处理部分的相应软件，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。