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The main interface contains menubuttons, command buttons,
dynamic entry texts, and two main wingets (windows). The upper winget is
a normal text editor, and specially for loading the multiple aligned sequences, i.e.,
the input file. The fonts for all 20 amino acids are colored automatically based on
the pre-defined color setting library, blue for
positive charged amino acid residues Arg,
Lys, and His;
red for negative charged residues
Asp and Glu;
green for polar residues Gln,
Asn, Ser, and
Thr; gold for
Cys; and black for the rest.
Results from MASIA are displayed in the lower winget.
Here is the GUI in actual size. * Performance Issues: If the file of mutiple aligned sequences is very big, the performance for automatic coloring can be expensive. We use different tags to configure font colores for individual amino acid residues, which means hundreds or thousands of different tags may be needed to make the job done. |
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- Definiton of Actions
click d-click t-click click+m drag B1 B2 |
Press one mouse button and release it without moving the mouse. Double-click within a short peoriod of time, usually a 500 milliseconds. Triple-click within a short peoriod of time. Hold down a modifier key (Shift/Ctrl) & click. Press mouse button, move the mouse, and release the button. The first mouse button (left). The second mouse button (left). |
- Operations of Actions
click B1 d-click B1 t-click B1 drag B1 click+m B1 clik+ctr B1 click B2 |
Set mouse cursor, clear the selection, set focus. Select the word under the mouse and set cursor at the beginning of the word. Select the line under the mouse and set cursor at the beginning of the line. Select arange between the cursor and the character under the mouse. Adjust the ends of the selection. Insert cursor no affecting the selection. Paste the selection at the mouse cursor. |
Control+N Control+O Control+S Control+P Control+Q Control+Shift+P Control+Shift+E Control+Shift+M Control+Z Control+R Control+X Control+C Control+V Delete |
Create a new file to be edit. Open a aligned mutiple sequences file. Save the file. Print content in the upper window. Exit MASIA. Open property library. Open exchange library. Open a macro file for running Masia. Undo the previous editor action. Redo the previously undone editor action. Cut the selection to the clipboard. Copy the selection to the clipboard. Insert text from the clipboard. Delete the selection, if any. |
One has to use macros to run MASIA. A macro consists of a set of MASIA commands in correct combination. The complete list of MASIA commands can be found in the command manual. The following are commands to run the MASIA through the GUI.
- characteristic name=string(4) [grpcrit=real(4.2)] [abbrev=string(1)]
Specifies the structural characteristics to be predicted.
The name=string(4) defines corresponding name of the structural characteristic of protein.
There are four choices: alph, beta, turn, coil for secondary structure prediction (SSP)
and two choices: insd, outs for hydrophobic/hydrophilic prediction of individual residue.
The grpcrit=real(4.2) specifies the criterion for structure/property prediction
from the analysis of "groups" which follow the curent command. The default value: grpcrit=1.00.
The abbrev=string(1) specifies the abbreviation character to be printed in the output.
The default characters:
