Table of Contents

User Settings

User settings such as adjusting memory settings, and changing structure display for hit alignment and highlighting can generally be made by accessing the Options window (Tools -> Options from the main menu).

1. Web browser selection and settings for proxy server selection.
2. Setting the page that IJC will display when it starts. The possibilities include:
   1. Welcome Screen
   2. Simple Federated Search page
   3. Any specified view (form view or grid view)
   4. None (IJC will open with the same windows open as when it last closed)
   There is also a setting that determines whether the window will open maximised (e.g. take up all the space within the main IJC window).

Keyboard bindings. You probably do not need to change these.

Various settings that affect IJC:

• Clipboard settings
• Confirmations
• Lists and queries
• Shared projects
• Startup Settings
• Structure display

Clipboard settings

These settings control how much data can be copied to the clipboard to prevent memory being exhausted when using large data sets

Confirmations

This section lets you set options for some confirmation dialogs that IJC uses. You can choose not to see these confirmations if you wish.

Lists and Queries

These settings control what happens to lists and queries.

• Number of temporary queries and lists to remember
• Maximum temporary list size that is created when a query is executed (to prevent memory exhaustion).
• Whether to truncate over-size lists or not to save them.
• Whether to create temporary queries when there are no hits or the whole data set is returned.
• Whether to clear the current query when 'Show All' is executed

Shared projects

Currently configured shared projects are listed, and you can add or remove shared projects. See the shared projects documentation for more details

Startup Settings

Memory settings can be adjusted to determine how much memory Java is allowed to use in IJC. If you are working with very large databases of structures, additional memory may be required. See Memory Usage and Settings for additional information.

To change memory settings:

1. Choose Tools -> Options from the main menu. The Options window appears.
2. Expand the Startup settings node.
3. Under 'Memory settings' set the memory values (in megabytes) for the application's starting and maximum sizes.
4. Click OK.
5. Restart Instant JChem

As an approximate guide work on the basis that IJC needs 64MB for its own use and each million structures that you have will take up approximately another 100MB.

Structure display options

When performing queries on structures, it is possible to specify how the found substructure is displayed by setting 'hit highlighting' and 'hit alignment'. Hit highlighting can be used to display the part of the structure that matches the query structure in a different colour. Hit alignment refers to rotating the hit structure so that it is displayed in the same orientation as the query structure. Typically both are used together, but each can be used on their own, or neither can be used. These only apply to substructure searching.

To change structure display:

1. Choose Tools -> Options from the main menu. The Options window appears.
2. Expand the Structure Display node.
3. In the Hit highlighting and alignment default drop-down list, specify whether highlighting and alignment are to be active.
4. In the Hit color drop-down list box, select a color to identify hit structures.
5. In the Non-hit color drop-down list box, select a color to identify structures that do not match the query structure in a performed query.
6. Click OK.

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