An alignment may be saved in its entirety as a bitmap image file, for use in document processing software, graphics software or for printing. A number of standard image file formats are supported: bmp, xpm, xbm, png. You can specify the size of the image to be saved in terms of pixels or millimetres.

To save an alignment as an image, right-click over the alignment to pop-up the context menu and choose Save alignment as an image, or choose Save as an image from the File menu. The Alignment output options dialog will appear:

From this dialog, you can determine the appearance and output size of the alignment. The first group of options controls whether the labels or the position key will be included in the image, and whether any motifs or breakpoints that are set will be drawn. To omit any of these features from the final image, un-check the appropriate box.

The second group of options controls the size of the image to be saved. You can specify an appropriate image size in either pixels or mm by:

1. Choosing the desired units from the drop-down box.
2. Entering a value in either the width or height boxes.

When altering the either the width or height, the aspect ratio of the alignment is maintained, and the corresponding dimension will be automatically updated for you. The width or height values may be rounded slightly to accommodate the entire alignment. Once you are ready to generate an image, click on the OK button.

The file save dialog will appear once the image has been generated; note that for large alignments, this may take a few seconds. Choose the appropriate image file format, enter a suitable name to save the image file as and click on the Save button.

An alignment may be printed out to any standard printer attached to your system. Alignments may be printed in colour, and on any paper format your printer supports.

You can specify the output size of the alignment in terms of pixels or millimetres. If the alignment is too large to fit the chosen paper size, CINEMA will print it in sections spread over an appropriate number of pages. These pages may subsequently be joined to recreate the entire alignment.

To print an alignment, right-click over the alignment to pop-up the context menu and choose Print entire alignment, or choose Print from the File menu. The Alignment output options dialog will appear:

From this dialog, you can determine the appearance and output size of the alignment. The first group of options controls whether the labels or the position key will be included, and whether any motifs or breakpoints that are set will be printed. To omit any of these features from the alignment, un-check the appropriate box.

The second group of options controls the size at which the alignment will be printed. You can specify an appropriate print size in either pixels or mm by:

1. Choosing the desired units from the drop-down box.
2. Entering a value in either the width or height boxes.

When altering the either the width or height, the aspect ratio of the alignment is maintained, and the corresponding dimension will be automatically updated for you. The width or height values may be rounded slightly to accommodate the entire alignment. Once you are ready to print, click on the OK button.

The standard print dialog will appear. Choose and configure an appropriate printer on the OK button to continue with printing.

Selecting the appropriate print format

In most cases, The Choose print format dialog will now appear, and you will be given the option of printing the alignment in one of two different styles:

1. Wrap the alignment over the page: the alignment is split into page-wide sections, which are printed vertically down the page. This style is the most appropriate for long, thin alignments, and makes the best use of the available page space.
2. Tile the alignment: the alignment is printed "as is", being split up into a set of page-sized tiles, each printed on a separate page. This style is most appropriate for alignments with very large numbers of sequences, and for producing posters - the tiles may subsequently be arranged, jigsaw-fashion, to recreate the alignment.

The Choose print format dialog gives an illustration of the different printing styles, and allows the user to choose the most appropriate. Click on the desired print style with the left mouse button, and select the Print button to start the printing process.

A colour scheme is the set of colours used for the visualisation of either a protein or a DNA sequence alignment.

In CINEMA, each alignment view has a unique colour scheme associated with it, by default either the standard protein or DNA sequence colour schemes that are provided. Using the Colour Scheme Manager, however, it is possible to customise the colour scheme for a particular alignment view, load an existing alternative colour scheme and save any customisations for future use. Thus, with CINEMA it is possible to visualise a sequence alignment using a number of different colour schemes simultaneously.

To edit the colours scheme for a particular alignment choose Edit colour scheme from the Edit menu. The Colour Scheme Manager dialog will appear:

This dialog shows a list of the residue symbols used in the current alignment, and the colour associated with each symbol. To change the colour associated with a residue:

1. Double-click on the block containing the residue symbol whose colour you wish to change
2. The Select Colour dialog appears. Use this dialog to select or generate the required colour.
3. Click on OK to accept the new colour. The current alignment view will be updated to reflect this change in colour scheme.

Once you have finished updating the colour scheme of your alignment, click the Apply button to dismiss the dialog and continue. Customised colour schemes may be saved for subsequent use by clicking on the Save button and choosing a suitable name. Similarly, an existing colour scheme may be opened for the current alignment view by clicking on the Load button and choosing the appropriate colour scheme file.