Technical FAQs

• Which platforms are supported?
• How can I trace problems with my Relibase+ installation?
• How do I obtain and install data updates?
• When I complete a search, a text file is displayed in the browser window.
• Why is the 3D sketcher not appearing on my system?
• The http data update package removed my symbolic links, how do I avoid this happening?
• I get a "404 Page not found" when I select Help -> Contents in Cavity Viewer
• Selecting superposition from a sketcher 3D query produces an error or no superposition plots
• Starting the Relibase+ 2.0 or 2.1 server with data update 35 or with multiple databases on IRIX causes the server to crash
• Relibase data updates fail with an error message similar to "sort: open failed: +4: No such file or directory"
• How do I enable command line history in relipython for Relibase+ 2.2?
• How do I delete an entire Relibase 3 database at the command line

Which platforms are supported?

Server:

The Relibase+ 3.1 server installation is supported on the following systems:

• Linux - Intel Compatible, 32-bit:
  • RedHat Enterprise 4 and 5
  • SuSe Linux Enterprise [Desktop|Server] 10
  • Debian 4.0, 5.0
  Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.

The total disk space required is approximately 200 GB (1 GB software). At least 2 GB physical RAM and 2 GB swap space are also highly recommended.

For details on the supported platforms for the Relibase+ client, please see the FAQ pages for Hermes.

Relibase has been tested when installed natively on these platforms. Use with emulators, including virtual machines, has not been tested & is not supported.

How can I trace problems with my Relibase+ installation?

The Help page within Relibase+ contains a troubleshooting section which can help you to identify any problems that you may be experiencing wiht Relibase+. This includes PHP diagnostics and Apache logs (for the httpd server bundled with Relibase+).

How do I obtain and install data updates?



Relibase+ data updates may be obtained in one of two ways:

Automated via FTP - On your Relibase+ server, with the Relibase+ environment sourced, run the command

relibase -data update

to obtain and install the latest data updates automatically from our update servers. Use of this method will require your server's IP address to first be logged with us.

Manually via download from our website - Download the data updates from our website Protected Downloads section. You will require your Relibase+ username and password details for access to these downloads. Once obtained, each update may be installed by following the instructions given on the download page.

Please contact admin@ccdc.cam.ac.uk for further details or assistance with obtaining access.

When I complete a search, a text file is displayed in the browser window.

The Relibase+ http server needs to have a mime type set up in order to handle Relibase's rlbcoor and reliview file types correctly. If these mime types are not set, a browser will treat the file as plain text and so display it in the browser window, when it should be displaying the structure with rasmol. Ensure that your http server has the following mime types set:

chemical/x-relibase rlbcoor

chemical/x-reliview reliview

For Apache servers, this will need to be set in your mime.types configuration file.

Why is the 3D sketcher not appearing on my system?

The 3D sketcher application requires the Java Runtime Enviroment (JRE) to have been installed on you system.. The latest java run time for your client system can be obtained from http://java.sun.com. Please note that Relibase+ 2.0 requires JRE 1.4.2 or higher.

The http data update package removed my symbolic links, how do I avoid this happening?

The http data update package requires the subdirectory structure of the $RELIBASE_ROOT/DATA directory to not be symbollic links, otherwise the unzipping of the file will overwrite these symbolic links when copying the data files. There are several solutions to avoid this problem:

1.If the data needs to be in a remote location, ensure that all of the data is in this one location, i.e. that the entire DATA directory remains intact and a single symbollic link to this remote DATA directory is created in $RELIBASE_ROOT.

2. Keep the DATA directory and all sub-directories local and instead create symbolic links in $RELIBASE_ROOT/DATA/DB to each remote data file seperately.

3. If the DB subdirectory must remain a symbollic link, before applying the data update make a note of where it is linked to (refered to below as REMOTE_LOCATION), then after application follow these steps:

mv $RELIBASE_ROOT/DATA/DB $RELIBASE_ROOT/DATA/DB_temp

ln -s REMOTE_LOCATION/DB $RELIBASE_ROOT/DATA/DB

mv $RELIBASE_ROOT/DATA/DB_temp/* $RELIBASE_ROOT/DATA/DB

rmdir $RELIBASE_ROOT/DATA/DB_temp

I get a "404 Page not found" when I select Help->Contents in Cavity Viewer

To resolve this, please download and apply the cav_doc.tar.gz patch

cd $RELIBASE_ROOT
gzip -dc cav_doc.tar.gz | tar xf -

Selecting superposition from a sketcher 3D query produces an error or no superposition plots

This error can occur if you have updated to version 2.1.1 of Relibase+ before 18th Spetember 2006 (when this problem was resolved in the patch files).

In order to resolve this, run the following command:

cp $RELIBASE_ROOT/php_src/disp_sub3d.php.2.1.0 $RELIBASE_ROOT/php_src/disp_sub3d.php

to replace the new 2.1.1 file with the old (correct) 2.1.0 version.

Starting the Relibase+ 2.0 or 2.1 server with data update 35 or with multiple databases on IRIX causes the server to crash

This error can occur if you have updated to data update 35 and/or are running Relibase+ with multiple databases on IRIX. The problem is caused by the default limit for file descriptors of 200 on IRIX systems.

The solution is to increase this limit. Before starting the Relibase+ server, enter the command:

limit descriptors 400

This should allow you to run the Relibase+ server normally. We also recommend that this command be added to your $RELIBASE_ROOT/bin/relibase.setup script to remove the need to manually enter it each time you start the Relibase+ server.

Relibase data updates fail with an error message similar to "sort: open failed: +4: No such file or directory"

This problem may be observed on newer linux versions, such as RedHat Enterprise 5, and is due to some functionality of the system "sort" command being made obsolete.

The solution is to edit the file download.pl and edit the line:

open(FULL_NEW,"| sort -nr +4 | uniq > $FULL_TMP_FILE");

to

open(FULL_NEW,"| sort -nr -k 5 | uniq > $FULL_TMP_FILE");



How do I enable command line history in relipython for Relibase+ 2.2?

You will need the readline4 library installed on your system to get command line history in relipython for Relibase+ 2.2. The method for obtaining this will vary depending on your operating system:

Linux
Version 4 of readline should already be present in most older Linux distributions. If you are using a newer linux distribution, you may only have readline library version 5, in which case you will need to download and install a package with the older version. The package name will vary depending on the linux distribution, i.e. for SuSe 9.x you would require compact-readline4.

IRIX
You can download and install readline from the SGI freeware website.



How do I delete an entire Relibase+ 3 database at the command line

These instructions are for Relibase+ 3 only

In some cases, you may wish to delete and entire in-house Relibase+ database.

Download cli_delete_domain.py.gz , uncompress it, and copy it to
$RELIBASE_ROOT/relibase_htdocs/reli-cgi/

You will need the Relibase+ environment set up, using either
. $RELIBASE_ROOT/bin/relibase.setup.sh or
source $RELIBASE_ROOT/bin/relibase.setup, then run:

  relipython $RELIBASE_ROOT/relibase_htdocs/reli-cgi/cli_delete_domain.py DATABASE

replacing DATABASE with the name of the database that you wish to delete.