In this example, we are going to compute a set of basic analyes to a 10 ns molecular dynamics simulation of a Serine Hydrolase ( pdb code: 1eve). When choosing Analysis as input type, the bottom part of the screen (the one corresponding to Analysis, -Base Trajectory-) will be enabled. Then, at the Input Type drop-down selector, just under the description, you should choose the option Analysis (MD Trajectory). You will be asked for a small set of data and input files: First of all, you may fill in a project title and a description (optional) at the top part of the form. In this tutorial, we will see an example of an Analysis project. MDWeb user can choose between two different kinds of inputs, Simulation and Analysis. Now, we are ready to start our first MDWeb analysis project. In this workspace, all projects of the user will be shown. Once logged in, the user workspace appears. Registration process will just take a minute -> Registration. We strongly recommend working as a registered user, as it has some important advantages.Īnonymous user's projects are completely removed once the user is disconnected and also when session expires (after some minutes of inactivity), and therefore working as anonymous user is only suited for a first impression of the web server. The first thing to do is to choose between working as an anonymous user or alternatively as a registered user. With this short tutorial, you will be able to upload a trajectory and run a set of analysis, checking for example the stability of your system or information about flexibility. Specific instructions are in this page in Jmol Wiki.MDWeb provides a friendly environment to analyse your own generated molecular dynamics trajectories. Then decompress (some of) its contents and put them into the folder where you are authoring your web pages. As a web page author, you need to extract the jsmol.zip file included in the downloaded package,.Nothing will be installed in your computer and there are no security concerns. The necessary files will be retrieved at the same time the web page is being read. As a user, you don't need to install or even download Jmol to be able to see web pages that use JSmol.To use the JSmol object embedded inside a web page:.Double-click on the Jmol.jar icon (or file) and it will run.Put it in any folder you like (such as c:\Program files\Jmol\, or even in My documents or in a USB stick the location You only need to extract the Jmol.jar file from the downloaded package.To use the Jmol Application (stand-alone program that runs in your computer):.Jmol isn't really installed as other programs are, but here is a brief description of how to put it into use: It is recommended, if possible, to install the latest Java version from Oracle.Īnd following instructions therein. The desktop standalone Jmol application requires Java 1.4 or higher. This includes tablets and smartphones, although performance may be slow on these devices. ![]() The JSmol object will run on any modern web browser. (Look under the Jmol heading for the link whose name ends in binary.zip or ,ĭepending on the format you can decompress in your computer.) Requirements If you are interested in an older version or you prefer a It can be downloaded from SourceForge at this direct
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