CINEMA can be used in conjunction with the Ambrosia 3D structure viewer, enabling simultaneous visualisation of a protein in terms of its sequence and its structure. Ambrosia is one of the other main Utopia applications and will have been installed on your system at the same times as CINEMA. The two applications are able to communicate with each other, and CINEMA can effectively be used to "drive" Ambrosia, allowing the user to:
- Instantly show the structure of a particular sequence
- Highlight regions of interest along the sequence and have these regions simultaneously highlighted on the structure
- Display on that structure any annotations that are being shown with the sequence
Note that using CINEMA collaboratively with Ambrosia is still very much a work in progress for this release, and the functionality provided is both limited and fairly experimental. Future releases will see, amongst other advances, full two-way communication, with Ambrosia able to direct CINEMA, and greater flexibility as to the types of data that can be visualised simultaneously in the two applications.
Before the structure of a protein can be opened up with Ambrosia, the following conditions must be met:
- Ambrosia must be running at the same time as CINEMA. See the Ambrosia documentation for details of how to start Ambrosia on your system.
- The sequence must have structural information that can be visualised. Currently, this means that only proteins from PDB (either local PDB files, or those obtained remotely from the database.) can be visualised with Ambrosia.
- The alignment that contains the sequence you wish to show in Ambrosia must first be saved to disk.
To open up a structural view of a sequence, right-click the mouse over the sequence to call up the context menu, and choose Show structure of "protein-name"... (If this menu item does not appear, then the selected sequence either has no associated structural information, or CINEMA cannot presently interpret it). An Ambrosia window will appear displaying the structure of the selected protein. You can choose show the structure of as many of the sequences in an alignment as is necessary, with each opening up in its own window.
Please refer to the Ambrosia User Guide for details of using Ambrosia.
Once Ambrosia has been instructed to open a structural view onto a protein sequence, it is then possible to select regions of a sequence, and have those regions automatically highlighted on the structure. To select a region, first click on the Selection icon to switch to Selection mode
and then:
- Position the mouse pointer over a residue in the sequence, and, with the left mouse button held down, drag the mouse pointer left or right to select a group of residues.
- As you do this, the selected residues will be automatically highlighted in the structural view.
Note that any gaps in the selected region of the sequence will be ignored in the structural view.
When using Ambrosia to visualize the structure of a particular sequence, any annotations that are displayed in CINEMA will, where appropriate, be automatically shown in the structural view. This allows for direct comparison of the annotated sequence and structure for a particular protein.
Generally, the structural view will only be able to display one annotation at a time, even though the alignment view my be showing several annotations at once for the sequence in question. As each further annotation is shown in CINEMA, it will replace the annotation currently active in the structural view. In such situations, Ambrosia may be instructed to re-show a particular annotation simply by clicking on that annotation in the alignment view.