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Technical FAQs
 Which platforms are supported?
Client:
The IsoStar 2.1.3 client executables, supplied with the 2012
release of the CSD System, are supported on the following platforms and
operating systems:
- Windows - Intel compatible Windows XP/Vista/7
- Linux - Intel compatible, 32 bit:
- RedHat Enterprise 4, 5, 6
- SuSE Linux Enterprise [Desktop|Server] 10, 11
- Debian 4, 5, 6
Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.
- Mac Intel compatible:
- Mac OS X 10.5, 10.6, 10.7
Server:
The IsoStar 2.1.3 server (including IsoGen), supplied with the 2012
release of the CSD System, is supported on the following platforms and
operating systems:
- Linux - Intel compatible, 32 bit:
- RedHat Enterprise 4, 5, 6
- SUSE Linux Enterprise [Desktop|Server] 10, 11
- Debian 4, 5, 6
Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.
Note: the IsoStar server is not supported on Mac OS X or Windows operating systems.
IsoStar has been tested when installed natively on these platforms. Use with emulators, including virtual machines, has not been tested & is not supported.
If you choose to use a version other than those listed above we cannot
guarantee that IsoStar will work correctly, although we will attempt to
assist you with any problems you may encounter.
How do I obtain the IsoStar client?
The IsoStar client package is distributed with the CSD software installation CDs of the CSD System, not with the IsoStar Server installation CDs. For Windows a separate IsoStar client installer can be
accessed from the Installer menu displayed when the Windows CD is run. For UNIX the IsoStar client is installed together with the other CSD software components
(e.g. ConQuest, Mogul etc.). The UNIX script for launching the IsoStar client is run_isostar and is located in $CSDHOME/bin.
Alternatively the IsoStar client is available as a standalone download (you will require your CSD site number and confirmation
code to download the client from this site).
How do I set up my
browser to view IsoStar scatterplots?
In order to view scatterplots in a Web browser you must configure it to use the IsoStar client as a helper application for files with a MIME type of
chemical/x-isostar. The IsoStar 2.0.1 client is installed as a part of the CSD System (together with Mercury, ConQuest etc), or is available as
a standalone download (you will require your CSD site number and confirmation code to download the client).
Once installed, the run_isostar script must be associated with your web browser. For example with Firefox 1.5:
- Start Firefox
- Select Edit
- Select the Downloads tab and click on View and Edit Actions under Download Actions. A pop-up should appear.
- Ensure that any old entries for IsoStar .istr files are removed from the list of actions. Close all of the pop-up windows and return to the
Firefox Browser.
- Navigate to the IsoStar 2.0.1 Home page, then to any scatterplot link and click on it. A dialog box will appear.
- Select Open With and then Browse.
- Select the run_isostar script located in the bin directory of either your CSD System installation, or an installed copy of
the IsoStar client download package.
- Check the "Do this automatically from now on" box to avoid having to go through this process again for subsequent scatterplots.
Note that the procedure detailed above will be similar but slightly different for later versions of Firefox (e.g. the initial dialog to view
is under Tools and then Options instead of Edit and Preferences. Other browsers may require you to set up the MIME types
directly:
- Type: chemical/x-isostar
- Suffix: istr
- Helper Application: {PATH_TO}/bin/run_isostar
Why do I just get a load of text in my browser window when trying to view a scatterplot?
The most likely cause of this type of problem is that your http server has not been correctly configured to distribute IsoStar
scatterplots as mime type chemical/x-isostar. Instead, they are being sent as plain text files, which your browser automatically
simply displays itself, rather than launching the IsoStar client.
For Apache servers, ensure that your mime.types configuration file has the following entry:
chemical/x-isostar istr
For other http servers, locate the appropriate file that configures mime types and edit in a similar manner.
Why can't IsoStar find
my database installation?
If you get a message similar to:
Could not find database files : dir home
child process exited abnormally
then IsoStar can not find the Cambridge Structural Database. This message
will typically appear when you are trying to Hyperlink.
IsoStar tries to find the database in several different ways.
- First it checks the environment variable CSDNAME. Typically
this will not be set and is reserved for times of desperation.
- Next, IsoStar checks CSDHOME. This should point to the
location of your installation of the CSD System. The database files
should be located in $CSDHOME/csd.
- If CSDHOME is not set, or appears to be set incorrectly, then
IsoStar checks CSDDIR. This variable will typically be set
by the IsoStar helper startup script. It should point to a directory
containing the database.
To solve the problem:
- Check whether CSDHOME is set. Type
echo $CSDHOME
If CSDHOME is not set then move to the next section.
If CSDHOME is set and you are reading this then it is
probably set incorrectly.
CSDHOME should point to a directory containing your installation
of the CSD System. This directory should contain a subdirectory called
csd. The subdirectory csd should contain three files:
asXYZbe.ind asXYZbe.msk asXYZbe.tcd
where XYZ is the version number of the CSD System.
If CSDHOME is set incorrectly then set it correctly, restart
your Web browser and try hyperlinking from a CSD Scatterplot.
- Check whether CSDDIR is set. Type
echo $CSDDIR
If CSDDIR is not set then move to the next section.
If CSDDIR is set and you are reading this then it is
probably set incorrectly.
CSDDIR should point to a directory containing three files:
asXYZbe.ind asXYZbe.msk asXYZbe.tcd
where XYZ is the version number of the CSD System.
If CSDDIR is set incorrectly then set it correctly, restart
your Web browser and try hyperlinking from a CSD Scatterplot.
- Look for a file in your home directory called .isostar_header.
This file may contain a line of the form:
csddir=<csdpath>
If the file does not exist or does not contain
the line described above then move to the next section.
If the file does exist and does contain
the line described above and you are reading this then csddir
is probably set incorrectly.
csddir should point to a directory containing three files:
asXYZbe.ind asXYZbe.msk asXYZbe.tcd
where XYZ is the version number of the CSD System.
If csddir is set incorrectly then set it correctly and try
hyperlinking from a CSD Scatterplot.
- Look in the file
<path>/isostar/d_<mach>/lib/isostar_header
where <path> contains your isostar software
directory and
<mach> is the type of your machine. Determine
<mach> by typing:
sh <path>/isostar/bin/csdmach.sh
The file <path>/isostar/d_<mach>/lib/isostar_header
will contain a line of the form:
csddir=<csdpath>
If you have got this far then csddir
is probably set incorrectly.
csddir should point to a directory containing three files:
asXYZbe.ind asXYZbe.msk asXYZbe.tcd
where XYZ is the version number of the CSD System.
Before correcting csddir in this file, you must consider
whether a change will impact on use of IsoStar from machines other than
your own. <path>/isostar/d_<mach>/lib/isostar_header
may be referenced from other machines for which the current setting
may be correct. If this is not an issue, then correct csddir
and try hyperlinking from a CSD Scatterplot.
If changing csddir in
<path>/isostar/d_<mach>/lib/isostar_header
is inappropriate then try one of the following:
- Override settings in
<path>/isostar/d_<mach>/lib/isostar_header
by putting a file called .isostar_header in the home directory of
the account from which you are running IsoStar. In this file,
put the line:
csddir=<csdpath>
where <csdpath> indicates correctly the directory containing
the three database files.
Note however that if you are
using the same account from different machines, doing this may mess
up IsoStar on other machines.
- Override settings in
<path>/isostar/d_<mach>/lib/isostar_header
and $HOME/.isostar_header by setting the environment
variable CSDDIR to point to the directory containing the
three database files before starting your Web browser and the
IsoStar software.
Unless you set CSDDIR in your personal or global
cshrc, profile or login files then they will
only persist within your current shell.
- If all of this fails to solve your problem then either:
What do I need to do to enable hyperlinking from the IsoStar client?
Note: If using the CCDC Apache server supplied with IsoStar, hyperlinking should already have been configured for the server. It should only be necessary to
correctly configure the client (see step 5 below).
Full details on what steps are required to enable hyperlinking from your own HTTP server are available from the Technical Help link from the Help tab of the IsoStar web
interface, which will contain details specific to your installation.
The following steps are required to enable hyperlinking from the IsoStar client:
- First you must copy the file:
<CDROM>/httpd/cgi/isostar_server.cgi
to the script directory of an http server (e.g. cgi-bin).
- Edit isostar_server.cgi as follows:
- Change ISOSTAR_ROOT to be:
<isosoft>/isostar
where <isosoft> is the location of the isostar
directory containing
an installation of the IsoStar software for the UNIX platform on which
the HTTP server is running.
- Edit <isosoft>/isostar/bin/xmlgen if necessary:
- Check the contents of
<isosoft>/isostar/bin/xmlgen
This will contain a line beginning
CCDC_TOOLKIT_ASER_DATABASE=
If there is no directory path specified on this line, or if it is incorrect, then change it
to indicate the
directory that contains your CSD database files. This is likely to be
equivalent to $CSDHOME/csd. Specify the full path to
this directory and the base filename of the current CSD database it contains. For example:
CCDC_TOOLKIT_ASER_DATABASE=/usr/local/cambridge/csd/as529be
- To test the CGI script, try accessing the following URLs:
- http://your.server/<cgi-bin>/isostar_server.cgi?check
- http://your.server/<cgi-bin>/isostar_server.cgi?check_license
- http://your.server/<cgi-bin>/isostar_server.cgi?csd_xml+aabhtz
- http://your.server/<cgi-bin>/isostar_server.cgi?pdb+0FOH01
Replace your.server with the address of your HTTP server and
<cgi-bin>
with the location of the directory containing isostar_server.cgi
(relative to the top directory of the HTTP server).
The first two URLs should display OK in your browser window;
the other two
should display MOL2 files.
- In the IsoStar client, select the "Hyperlink Server..." option from the "Options" pull-down menu and enter the server and script details that
correspond to your setup (this will be your.server and <cgi-bin>/isostar_server.cgi that you used in the preceding step to
test the script.
Hyperlinking in a PDB scatterplot from
IsoStar 2.1.3 fails with a "duplicate bond" error message.
This error will only occur if you are hyperlinking using your own IsoStar server - hyperlinking to CCDC's IsoStar server should work normally.
We have prepared a patch that will correct your IsoStar installation. Please download the file PDB.tar.gz
into your $ISOSTAR_ROOT/lib directory and unpack with the command: gunzip -c PDB.tar.gz | tar xvf - Please note that this download will require
your 2012 CSDS site number and confirmation code as username and password.
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