When the application is executed the following interface is shown:
ProtDCal main window
Table 1: Main screen details
Name | Description | |
A | Menu | Summary of commands for execution |
B | Toolbar | Frequently used commands. |
C | Panels | The indices, groups and aggregation_operator implemented in ProtDCal. |
The panels below the toolbar represent the three of the hierarchical levels described above (Modification Operators are accessed via the Options menu). When you mouse over each element, a brief text description pops up explaining its functionality. Panels (indices, groups and aggregation operators) are subdivided, according to their nature, into several subpanels.
The panel of indices is divided into four subpanels (Thermodynamic Indices for Structures, Thermodynamic Indices for Sequences, Topographic Indices, and Properties-based Indices).
Indices Panel
In the Topographic Indices subpanel, there are several weighted indices (starting with the letter "w"), that can be calculated using one or several weights for inter-residue contacts. The following figure shows the window intended for selecting the properties to be used as weights for contacts. This window appears every time one of these weighted indices is selected, in such a way that different properties can be selected for different indices. Alternatively, if many indices will use the same weighting properties, one could first select all the topographic indices at once by clicking the button 'Topographic Indices of Folded Protein States', which launches the properties window once, and then the user may deselect the non-desired indices. These indices will be identified in the outputs as follows: "index_name(weight)".
Weight Window
Other indices can be computed using "TAE Aminoacid Descriptor..." and "Other Indices..." buttons located at the end of the panel. The first option, calculates Transferable Atom Equivalent (TAE) indices available in: http://reccr.chem.rpi.edu/Software/Protein-Recon/TAE.doc..
The second option computes defined properties (see Creating new Properties)using the "Define new indices" option located in the menu "Option/Manage Indices". This options display the following window:
Select Indices Window
In this window the (), (ALL) and (
) buttons can select the indices previously defined.
In the panel of groups there are three subpanels enclosing groups by residue ID, properties and topographic features. Also with the "Others groups..." button is possible to select groups previously defined by the user (see Define new groups).
Groups Panel
Aggregation_Operator Panel