Registration will help us to keep you posted User support in the form of donations will help us toĬontinue the development of RasMol. The author(s) and do not necessarily reflect the views of the funding agencies. NIH National Institute of General Medical Sciences.Īny opinions, findings, and conclusions or recommendations expressed in this material are those of Work on RasMol has been supported in part by grants from the U.S. Members of the community are welcome to join us on the site. Is the external development site provided by SourceForge, Inc. For the convenience ofĬontributors to the RasMol project, an open source collaborative Of modifications provided by the community is done at theĪRCiB project at RIT. Maintenance of RasMol, much of the development, and integration The site itself is provided courtesy of Bernstein + Sons. Of users of RasMol and developers of open source versions of This site is provided for the convenience X3D standard is XML-based and supports visualization of 3D computer graphics.RasMol is a program for molecular graphics visualisation originallyĭeveloped by Roger Sayle. In this post, visualization capabilities of Jmol are exploited for generating the orbital imagery that uses open-source x3d format. Web Visualization of NBOs in x3d Format Latest The accompanying demo webpage can be viewed It is fully responsive and supports devices, such as phones and tablets. The site was recently re-build using the Bootstrap framework and LESS dynamic style sheet language. Those are then loaded into the web interface with the assistance of JSmol serving as a client backend.Īll files described in the post are available from the Download section of the Blog. A script is generated that writes the NBO surfaces into the corresponding jvxl files. Jmol macro files allow loading and visualization of NBO archive files (.31-.46). The required jvxl files are generated using the Jmol-NBO Visualization Helper featured below. With the help of css, JavaScript, and JQuery, "gallery-type" interaction with molecular and surface models has been implemented. The visualization is based on jvxl surface and structure files and it is supported by the JSmol. Steps for getting the key elements for building the website are described in the Blog. This blog explores Jmol-jvxl-based visualization of NBOs in a static website. Jmol visualization of formamide NBO Visualization Cornerĭynamic web visualization and jvxl surface files Latest It is mostly students of Organic Chemistry who will benefit from apps available at this web site, although I hope that professionals from other disciplines, such as computational chemistry and physical chemistry will find these topics useful as well. The main driver behind the Java apps, Jupyter Notebooks, and Java/Python workflows is to provide teachers, students, and researchers with simple tools for generating a wide variety of NBO results and visualizations without requirements of detailed knowledge of NBO keywords and Jmol syntax. To present results that include NBO orbital imagery, two methods employing jvxl and x3d files are described in building the "life" web-site display. Several workflows are available for download from the KNIME section. For more complex tasks involving multiple properties and visualizations, I prefer using the KNIME analytics and visualization environment. Many scripts and Jupyter notebooks are available from the corresponding section of these pages. To simplify the retrieval of NBO-related information from NBO result files, I opted for the Python language. Descriptions and examples still stay with the original blog posts. Since blog space is not the best place for storing and tracking apps, it was only a matter of time before I decided to move the app files and links to static web site. I wrote simple Java applications to assist with repetitive tasks accompanying the generation of Jmol scripts, macros and GENNBO inputs. Over the past few years, I have been posting blog entries discussing approaches to visualization of Natural Bond Orbitals (NBO) in an open-source Java molecular viewer, Jmol. This website attempts to bring useful tools of Natural Bond Orbital analysis into one place while encouraging readers, researchers, and teachers to share their experience and ideas to further facilitate analysis, interpretation, and visualization of NBOs. NBO description of chemical bonding conforms closely to the localized 2-electron/2-center concepts of Lewis and Pauling, both descriptions being a cornerstone of freshman chemistry. Natural bond orbital (NBO) analysis is a powerful method for formulating intuitive chemical hypotheses from otherwise complex quantum mechanical description of the molecular wavefunction.
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