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jRAMA+:
A Web-Based Java Viewer for TALOS+ Torsion Angle Predictions

Current version: 2.1 Build 2014.04.01
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Java RAMA+ Notice:
Your browser does not support Java, or Java is not installed and enabled. Follow the directions below to install and enable Java, or try using a different web browser.

This web page provides access to a Web-Based Java version of the RAMA+ viewer, which is part of the TALOS+ System for predicting protein phi and psi torsion angles using backbone chemical shifts. The RAMA+ viewer can be used to view results produced by the TALOS+ Prediction Server. It can also be used to view results produced by any installation of TALOS+ Version 2.30 or higher.

The Java RAMA+ viewer will work with most web browsers, and currently requires that Java Version 1.5 and above is installed and enabled in the web browser. If you have problems using the viewer, try updating the installed version of Java, or using a different web browser. Instructions on installing, enabling, and testing Java are given below.
NOTE: Java Version(s) 1.7.0 has enhanced its security to block self-signed and unsigned applets on (default) High Security Setting. In order to run java RAMA+ viewer in a browser, users have to manually adjust/lower Java security level to Medium Security Setting, see details at http://www.java.com/en/download/help/jcp_security.xml

The Java RAMA+ viewer can be run locally as well on any computer without using web browsers. To do this, the viewer file (rama.jar) needs to be downloaded (here) and stored to the local computer (for which Java must be firstly installed). The viewer then can be excuted by typing a command line "java -jar rama.jar" (for unix-based systems) or simply by clicking the rama.jar file (for Windows systems).

The Java RAMA+ viewer also requires that the six result files produced by TALOS+ are saved together in the same directory. These files are used as input by the viewer. Details about this are below.

If the TALOS+ logo image appears at left, this means that Java is installed and enabled. You can click on the logo image to start the Java RAMA+ Viewer. When the viewer first starts, a Java Security Window might appear, asking for your permission to run the viewer applet.

If Java is not installed and enabled, no TALOS+ logo image will appear at left. Instead, a notice will be displayed stating that Java is not installed or enabled. If this happens, consult the instructions at the bottom of this page to install and enable Java in your browser.


How to Use the Java RAMA+ Viewer

Start the Java RAMA+ Viewer by clicking on the TALOS+ logo image above. When the viewer first starts, it might display a Java Security Window similar to the one shown here. Use the given option to run the application:

java Security Window

When the viewer starts, it will display a single window with a Ramachandran map. Follow these steps to use the viewer to display existing TALOS+ results:

  1. In order to use the viewer, the existing TALOS+ result files must be saved together in the same directory. Specifically, the following files are required:

    • pred.tab
    • predAll.tab
    • predAdjCS.tab
    • predSS.tab
    • predS2.tab
    • predABP.tab

  2. Click on the File menu and select Open Prediction Files... this will create a file browser window. Use the file browser to find and select the TALOS+ prediction summary file pred.tab ... only this one file should be selected; the viewer will find the other files based on the specified location of the pred.tab file. Once this file is selected, the viewer will read all the input files, and display a Residue Sequence window, a Secondary Shift Distribution window and a window graphing both the RCI Chemical Shift S2 Order values and the Predicted Secondary Structure. Illustrations of these viewer windows are shown below. For more about the interpretation and use of the viewer graphics, see the TALOS+ Web Page.

  3. If a reference PDB structure is available, click on the File menu and select Open Reference Structure... to find and select the PDB file using the file browser. When a reference PDB file is selected, its phi and psi backbone torsion angles will be displayed in the Ramachandran maps as blue squares.

  4. Use the viewer to inspect TALOS+ prediction results. If desired, you can also use the viewer to make modifications to the prediction results, by toggling which database entries are used to form a prediction, or by changing the classification of predictions (Good, Ambiguous, etc.). Prediction tables modified through the interactive display can be viewed and saved by clicking on the Display menu and selecting the Output File Window option.

If there are problems starting the browser, or problems selecting the prediction input, it may be that you need an updated version of Java, as described at the bottom of this page. You might also need to use a different version of your web browser or a try a different web browser application or even a different system. For example, try a system with Internet Explorer if a system with Firefox is problematic.

        rama File Menu           rama File Browser

all rama windows


How to Install Java and Enable Java Applets in your Web Browser

If Java is already installed and enabled, you can test your version of Java by clicking here to go to the Java Test Site. At the time of this writing, the current Java distribution is v1.6; if the Java Plug-in version is v1.5 or greater, you are ready to run the Java RAMA+ Viewer.

If Java needs to be installed or updated on your system, you can follow the instructions on the Java Test Site used above. Alternatively, you can go to the Java Download page and follow the instructions there.

In addition to installing Java, you might have to manually enable the use of Java in your web browser. You can check the Java Help Site for instructions on how to enable Java in different browsers, or follow the instructions listed below for three browsers:

Internet Explorer

  1. From the Tools menu, select Internet Options.
  2. In the Internet Options window, select the Advanced tab.
  3. In the Settings list, scroll down to the section marked Java (Sun)
  4. Enable the check the box next to the entry for the current Sun Java JRE version.
  5. Next, select the Security tab, and click the Custom Level button.
  6. In the Settings list, scroll down to the entry Scripting of Java applets make sure the Enable radio button is selected.
  7. Click the OK button to save the new settings.
  8. Restart the computer.

Firefox

The details for enabling Java depend on the version of Firefox. At the time of this writing, the current version of Firefox is v3.6.12. For Firefox 3.6, you can enable or disable all plug-ins including Java via Tools > Add-ons > Plugins. To enable Java for Firefox 3.5 and below:

  1. From the Edit menu, select Preferences.
  2. In the Preferences Window, select the Content tab.
  3. Select the checkboxs to Enable JavaScript and Enable Java.
  4. Click the Close button to save the new settings.
  5. Restart the computer.

Safari

  1. From the Safari menu, select the Preferences option.
  2. In the Preferences Window, select the Security tab.
  3. Select the check box to Enable Java.
  4. Select the check box to Enable JavaScript.
  5. Restart the computer.

By using this web site and its applications you are agreeing to the Terms of Use.

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Java RAMA+ software created by Yang Shen
last update: May 23 2012 by sy