Current version: 3.03 Build 2016.06.10
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This web page provides access to a Web-Based Java version of the
RAMA viewer, which is part of
the TALOS-N 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-N Prediction
Server. It can also be used to view results produced by any
installation of TALOS-N Version 4.0 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 in Java Control Panel -> Security.
Note: Java Version(s) 1.8.0 has further enhanced its security and disabled the
Medium Security level in Java Control Panel -> Security, users then have to
manually add our site http://spin.niddk.nih.gov/bax/ to the Exception Site
List in the Java Control Panel -> Security,
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 seven result files
produced by TALOS-N are saved together in the same directory. These files
are used as input by the viewer. Details about this are below.
If the TALOS-N 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-N 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.
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How to Use the Java RAMA Viewer
Start the Java RAMA Viewer by clicking on the TALOS-N 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:

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-N results:
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In order to use the viewer, the existing TALOS-N result files must be saved
together in the same directory. Specifically, the following files are
required:
pred.tab
predChi1.tab
predAll.tab
predAdjCS.tab
predSS.tab
predS2.tab
predABP.tab
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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-N 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 Chi1 Rotamer Prediction 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-N Web Page.
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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.
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Use the viewer to inspect TALOS-N 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.
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
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From the Tools menu, select Internet Options.
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In the Internet Options window, select
the Advanced tab.
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In the Settings list, scroll down to the
section marked Java (Sun)
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Enable the check the box next to the entry for the current
Sun Java JRE version.
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Next, select the Security tab, and click the
Custom Level button.
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In the Settings list, scroll down to the
entry Scripting of Java applets make sure the
Enable radio button is selected.
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Click the OK button to save the new settings.
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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:
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From the Edit menu, select Preferences.
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In the Preferences Window, select
the Content tab.
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Select the checkboxs to Enable JavaScript and Enable Java.
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Click the Close button to save the new settings.
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Restart the computer.
Safari
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From the Safari menu, select
the Preferences option.
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In the Preferences Window, select
the Security tab.
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Select the check box to Enable Java.
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Select the check box to Enable JavaScript.
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Restart the computer.
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