@*~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:
-
Important key strokes you should know:
- Ctrl+C Copy text
- Ctrl+V Paste text
- Ctrl+X Cut Text and add it to the Clipboard (German Zwischenablage see WIKI:Cut_paste)
- Ctrl+F Find text pattern
- Ctrl++ Zoom in (Also Ctrl+mouse wheel)
- Ctrl+- Zoom out
- F1 Help
- Shift+→ or Shift+←: In text processors the cursor is moved and a text segment is selected.
In list elements like the file browser, one item can be selected by mouse click and neighboured elements can be selected with the Shift plus keyboard Arrow keys.
In the alignment panel and all 3D views this selects consecutive amino acids.
- WIKI:Context_menus. For example right click a file in your file browser.
- WIKI:Drag_and_drop. For example drag a file to another location.
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:
- Ctrl+A selects all.
- Left-click one and Shift+click another sequence selects all sequences in between.
- Shift+↓ or Shift+↑ or Shift+PaDown or Shift+PaUp selects multiple sequences.
- Ctrl+click toggles selections
- Ctrl+F opens a dialog for text search on the sequence name or header text
Please try:
- Decrease and increase the height of the alignment panel.
- Change the order of sequences by dragging sequence names up and down.
- Drag them outside the application frame to copy the sequence files for example to the desktop.
- Get the context-menu by right-click.
- Read the balloon message of a sequence (Mouse pointer at the left margin of a sequence name).
- 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:
- Select an amino acid sequence from the alignment pane
- The alignment overview will also display that selection
- The blue focus area can be moved to navigate
- The alignment overview displays many features including the flashing cursor position,
residue selections, residue color code, rectangular selections, hydrophobicity and entropy
plots
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:
- Insert and delete gaps using the Space Bar, Delete key and Backspace key.
- Change two sequences simultaneously by selecting the two sequences.
- Insert exactly 13 white spaces by typing "1" "3" "space-bar".
- 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:
- Double clicking on the selection
- or menu item HTMLDOC_BUTTON:M_SEL_EDIT from the context menu. (Get context menu by right clicking the selection)
- or drag it and drop it on the same sequence.
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.
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