You need to have the Java Virtual Machine (JVM) installed on your computer to view the JAVA applets on this site. The signed Java applets will be displayed properly only when viewed in Internet Explorer and Netscape Navigator having Java plug-in installed.

The latest version of Java Runtime Environment (JRE) for various platforms is available from the SUN website http://www.java.com/en/download/manual.jsp . The latest version of Internet Explorer for the Windows platform is avalable from the Microsoft website http://www.microsoft.com/windows/ie/default.asp . Netscape Navigator can be downloaded for various platforms from Netscape's website http://wp.netscape.com/download/full_install.html .

The minimum version of JRE which is required for the applets to run is 1.4.2.04. Local copies of JRE 1.4.2.04, Internet Explorer 6 and Netscape 7.1 are available for download from our server for the platforms on which our applets have been tested. 3-D Structure viewers RasMol 2.7.2.1.1 and Chime 2.6 are also available for download from our server for their respective platforms:

Once the JRE has been properly set up on your computer, you will be prompted to accept security certificates signed by "Dr. Pinak Chakrabarti" when your browser attempts to launch the applets. This is to enable uploading of files by the users. No personal information will be retained from the user's computer on our server other than the data he/she voluntarily submits, which will be deleted periodically.

The users should submit the PDB files in plain text format only. Any other file format will not be accepted by our server and you will receive an error message. The filename can be of any length, but the extension (following the period) has to be of exactly three characters. There is also an upper limit of 2 MB on the filesize. Once the file is submitted, several programs are run on it on our server and the user ultimately receives a single web page showing the secondary structure information for all the chains as provided by the DSSP program. Additionally, all the interface residues are shown and the user has the option of dissecting the residues into patches or core/rim regions. The software expects the residue numbers (against the co-ordinate records) in the PDB file to be in serial order. Negative residue numbers or using using the same residue number for multiple residues will cause problems.

Under heavy traffic conditions and depending on the size of your PDB file, you might be required to wait as long as 10 minutes from the submission of the PDB file to the display of the results. If you have any query, please drop a mail to to Dr. Pinak Chakrabarti (pinak@bic.boseinst.ernet.in).

Disclaimer

The software is provided as is. Though the software has been tested successfully on a large number of files, we cannot guarantee that the system is fool-proof. Any comments or suggestions for improving the software or this site are welcome.

External Software Used

Public Domain:

NACCESS

DSSP

Copyrighted:

Java © Sun Microsystems, Inc . All rights reserved.

Internet Explorer © Microsoft Corporation . All rights reserved.

Netscape © Netscape . All rights reserved.

RasMol [ OpenRasMol site ] © Bernstein + Sons . All rights reserved. Other copyrights apply.

Chime © MDL Information Systems, Inc. . All rights reserved.