3.11 Energy dot plot
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3.11 Energy dot plot
The energy dot plot displays the superposition of all possible foldings within a user specified energy increment from the computed minimum. In this triangular plot, a dot in row i and column j represents a base pair between ribonucleotides i and j. In the UNIX versions, different colors are used to represent the different levels of suboptimality. The description of the VAX energy dot plot has already appeared in [16]. The description here will be for the IRIS version that runs only on a Silicon Graphics workstation, and for an X11 version developed for the DECstation 3100 (ULTRIX), but now running on the SGI IRIS, SUN4 and sparcstations, and the DECstation 5000.
In the IRIS specific version, a non-resizable, non-movable window that fills the entire screen is created in which the triangular energy dot plot is displayed along with other information. This window can be moved and resized in the X11 version, and does not initially fill the screen. Energy values are in kcal/mole, and the base pairs are displayed according to their historical numberings. Energy increments are entered by the user as integers in 10ths of a kcal/mol.
Interaction with the program is by means of the mouse and popup menus. The popup menu can be displayed by pressing the right mouse button. An item can be selected by moving the pointer to the desired selection and releasing the mouse button.
The ``Optimal score'' that is displayed in the dot plot is the minimum folding energy. The ``Energy increment'' is the highest deviation in kcal/mole from the minimum energy for which a base pair will be plotted. Thus all base pairs that are in foldings within this increment from the minimum folding energy will be plotted, consistent with the value of the ``minimum vector size for plot'' parameter (3.4). The energy increment is initially 0, so that only the optimal foldings appear at first.
- 3.11.1 Changing the energy increment
- 3.11.2 Selecting base pairs from the dot plot
- 3.11.3 Computing structures
- 3.11.4 Displaying the ``P-num plot''
- 3.11.5 Choosing colors for the dot plot
- 3.11.6 Creating a ``hard copy'' of the dot plot
- 3.11.7 Final details in the dot plot
Next: 3.11.1 Changing
the Up: 3. Methods
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Michael Zuker
Thu Nov 2 14:28:14 CST 1995