@*~RSC_HELP_TUTORIAL_INTRO This tutorial takes about 40 min and explains the basics of Strap.

Printing this tutorial: Click into the text to set the input focus and type Ctrl+P. This text will then appear in the Web-browser where it can be printed. If the web browser is not started, adjust the settings in the Preferences menu HTMLDOC_BUTTON:CUSTOM_webBrowser!.

Computer-Basics

HTMLDOC_OS_MAC{Macintosh differs slightly from other systems, for example the Command key is often used instead of Ctrl)}HTMLDOC_OS_MAC Consider a few elementary concepts of graphical computer systems. With the text processor and the HTMLDOC_OS_MAC{Finder}HTMLDOC_OS_MAC HTMLDOC_OS_WIN{File Explorer}HTMLDOC_OS_WIN HTMLDOC_OS_mac_win{file browser}HTMLDOC_OS_mac_win try the following:

The row headers

Push the button HTMLDOC_BUTTON:SBUT_TUTORIAL_LOAD_EXAMPLE_1D3D! - some example sequences are downloaded and appear in the alignment pane. The header of each alignment row shows the sequence name. Select sequences. Selected sequences are white on blue. Multiple item selection works in the standard way. Please try: Please try:
  1. Decrease and increase the height of the alignment panel.
  2. Change the order of sequences by dragging sequence names up and down.
  3. Drag them outside the application frame to copy the sequence files for example to the desktop.
  4. Get the context-menu by right-click.
  5. Read the balloon message of a sequence (Mouse pointer at the left margin of a sequence name).
  6. Change the order of sequences using short cut keys: Select sequences and type Ctrl+X or Ctrl+C. Select another row and type Ctrl+V to introduce the sequences here.

Aligning sequences

Select all sequences and click the tool button [Align all]. Initially, the alignment programs will be installed. When the computation succeeds, the sequences will be aligned. Strap automatically combines the default 3D and sequence methods to obtain the optimal alignment.

Alignment overview

Activate the Overview button left from the horizontal scroll-bar. The alignment overview is a powerful feature that allows visual navigation in large alignments. Please try the following exercises to get used to the alignment overview:

Editing the Alignment

Click in the alignment to get a text-cursor. Cursor navigation and text editing works like in MS-Word with the difference that only white space can be inserted or deleted, but the amino acids cannot be changed. See Keyboard commands.
Exercise:
  1. Insert and delete gaps using the Space Bar, Delete key and Backspace key.
  2. Change two sequences simultaneously by selecting the two sequences.
  3. Insert exactly 13 white spaces by typing "1" "3" "space-bar".
  4. Change the order of the sequences.

Copy-and-Paste and Drag-and-Drop (D&D)

Create a text file with the following text. Use any text editor. Save it as plain text file, not in Word-format.
  this is
  my amino acid
  sequence
Next try two alternative methods to drop this amino acid sequence into Strap: Drag-and-Drop text selection: Now select the entire text in the text editor.HTMLDOC_OS_WIN{Notepad does not work. Use Wordpad instead.}HTMLDOC_OS_WIN Drag the selection with the mouse into the Strap application. You will be asked for a sequence name.

Drag-and-Drop a file: Save the file as plain text. Avoid white space in the file name! Some text-editors like the default editor of Apple OS or MS-Word may cause problems by offering special formats rather than plain text. Do not save it in MS-Word- or HTML- or RTF format, it has to be plain text! The file will usually have the ending ".txt" thought for Strap the ending does not matter. Drag the file with the mouse and drop it into the Strap application. Drag and Drop is a key feature of Strap and is usually more convenient than the file browser opened with Ctrl+O.

Drag-and-Drop a file from file browser: Find the drop target HTMLDOC_ICON:IC_SHOPPING at the left of Strap. Click the icon and study the web page about Drag-and-Drop which appears in the browser. If opening the browser fails, check the settings HTMLDOC_BUTTON:CUSTOM_webBrowser!.

Residue selections

Please drag the mouse over some amino acids. This will create a residue selection. But, if the mouse crosses rows, a rubber band selection appears which is not what you want at the moment. You rather need to stay in one row while dragging.

Explore this selection: (I) Move the mouse over the highlighted residues. The underlining will start flashing and a balloon message appears. (II) Drag it to another aligned sequence. (III) Change the color using the context menu

If you select some other amino acids, the previous selection is lost. There can be only one mouse selection at a time. To overcome this limitation, this basic selection needs to be turned into a persistent one. Please try the following three alternative approaches: The generated selection can hold data shown as a table on double-click.
HTMLDOC_JCOMPONENT:HTMLDOC_JC_ResidueAnnotation_Balloon

Please add further annotations. For example enter a balloon message which will be displayed when the mouse pointer is over the selection.

Rubber Band selections

Create a rubber band selection by dragging the mouse over several rows. A white / red rectangle of marching ants appears. Change the size at its edges and corners. Several analysis tools optionally take the rectangle instead of the entire alignment. Study the rectangle's context menu.

Looking for a particular menu item

Supposed you want to sort sequences by similarity but you cannot find this program feature in Strap. The solution is a text search in the list of all menu items from the help menu: HTMLDOC_BUTTON:SBUT_ALL_MENUS! and HTMLDOC_BUTTON:SBUT_ALL_POPUP!. Perform a string pattern search (Ctrl+F) in these two lists. Identify the dialog to sort sequences!

Word completion with the Tabulator-key

Tab-word completion is a convenient feature and can be tested in the file Open box. Select "Open file ..." from the File menu or type Ctrl+O to open the file selector dialog. Focus the text field for manually typing file names and type only the first letter of the file name. Hitting the tabulator key will complete the file name. In case of ambiguity, it cycles through all possibilities.

Multiple Strap instances

Select all sequences. Start a second Strap session with a different project directory. Then drag the selected sequences to the other Strap Window. Not only sequences can be exchanged between Strap sessions but also residue selections.

Always floating on top

The main Strap window and all other windows can be set "floating on top" which means that they are not hidden by other windows even if they do not have the focus. Those windows are indicated by a "^" sign in the window's title bar. Some windows are initially in this state. To try this feature, set the input focus to the main application window by mouse click. Then type Ctrl-T. Type Ctrl-T again to get back to normal. *@