Page tree. Browse pages. A t tachments 0 Page History People who can view. Hide Inline Comments. Jira links. Jmol is an open source Java-based program for viewing molecules.
Warning Jmol can be difficult and time consuming to install. We suggest that you download Jmol directly from the CBM website to ensure you are using the correct version for creating physical models. You may click the link below to download Jmol. Jmol Version You need to have Java on your computer to run the desktop version of Jmol.
Jmol does not need to be 'installed', so once the Jmol file is in place on your computer, the program will be ready to use. Click on the Jmol. You may save the Jmol file you download in any convenient location on your computer.
Jmol does not need to be 'installed', so once these files are in place on your computer, the program will be ready to use. Click on the Jmol file to start Jmol on your computer.
Files you save in Jmol will be saved in the same file location as the Jmol file. Molecular structures can be determined through the use of X-ray Crystallography, Nuclear Magnetic Resonance NMR , or computer algorithm-based calculations. Once a structure has been determined, each atom in the structure is assigned an X,Y,Z coordinate to mark its location in 3-dimensional space. Molecular visualization software, such as Jmol, can then use the coordinates stored in a PDB file to create an interactive 3-dimensional visualization of a molecular structure.
We will be using Jmol to view the PDB file 1qys. In the top right corner of the website there is a search bar similar to the image below. This should bring you to the page for '1qys. Just below the search box on the right should be a list of four options similar to the image shown below. Click ' Download Files ' and you will see an expanded menu similar to the second image shown below. This file, named '1qys.
Note: It is a good idea to create a new folder for each molecule you explore to organize all PDB files, images, articles and other related work. If you don't need additional information about the PDB file or don't wish to save a copy of the file on your computer, you can 'call up' the file in Jmol without downloading.
Note: -y flag means to assume yes and silently install, without asking you questions in most cases. Package Description. Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules.
Jmol might be useful for students, educators, and researchers in chemistry and biochemistry.
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