@*~RSC_HELP_3D_CANVAS_NOT_DND
If you came here because you intended to drag a protein with the mouse:
This is not the right way to drag a protein.
You can start dragging a protein for example from the respective row header of the sequence alignment.
HTMLDOC_BUTTON:BUTS_MOVIE_Export_Proteins!
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@*~RSC_HELP_APPLET_LOCAL
Note:
3D Visualization in the web browser may fail.
This is because Java applets do not load data from the local file system.
Workaround - 3D visualization
- Install a local web server like Apache.
- Chose an output file within the directory of the web server, often /var/www/.
- In the browser, enter the respective URL which starts with http://localhost/.
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@*~RSC_HELP_STRAP_KEYSTROKE
The keyboard is used to move the alignment cursor and to introduced/removed alignment gaps.
Cursor Movements
← | Left |
→ | Right |
Ctrl+← | To first residue |
Ctrl+→ | To last residue |
Alt+→ | To next gap |
Alt+← | To previous gap |
Home | To first row |
End | To last row |
Ctrl+Home | To first residue |
Ctrl+End | to last residue |
Movement of the view-port
PgDown | Scroll down |
PgUp | Scroll up |
Shift+PgUp | Scroll left |
Deleting gaps
Delete | Delete gap right from or under cursor |
Backspace | Delete gap left from cursor |
Ctrl+Delete | Delete next gap right from the cursor |
Ctrl+Backspace | Delete next gap left from cursor |
Ctrl+Shift+Delete | Delete entire white space under cursor |
Ctrl+Shift+Backspace | Delete entire white space left from cursor |
Inserting gaps
Space | Insert gap under cursor |
Insert | Insert gaps until next residue in above row is reached. |
Ctrl+Ins | Remove gaps until previous residue in above row is reached |
Shift+Ins | Insert gaps until next residue in below row is reached |
Repetition number. Performing an operation n times
4 2 Space | Insert 42 gaps |
4 2 Delete | Delete 42 gaps |
Moving a sequence blocks, i.e. consecutive residues that are not interrupted by gaps.
> | Move block of consecutive residues to the right |
< | Move block of consecutive residues to the left |
Miscellaneous
HTMLDOC_OS_MAC{Ctrl+Command-F or Ctrl- }HTMLDOC_OS_MACF11 | Full-screen |
Ctrl+W | Close alignment panel |
Ctrl+K | Close sequence |
U | Upper Case |
L | Lower Case |
Appearance
Ctrl++ | Zoom in |
Ctrl+- | Zoom out |
Ctrl+* | Display letters in better quality |
Go to position
4 2 i | Move cursor to residue index 42 |
4 r | Move cursor to 4th row |
4 2 c | Move cursor to column 42 |
4 2 n | Move cursor pdb-number 42 |
Save / restore position
S | Save current cursor position |
s | Revert cursor position previously saved |
4 S | Save current cursor position to "4" |
4 s | Restore cursor position previously saved in "4" |
The mouse actions follow general conventions:
-
Sequence alignment
- Left-click sets the cursor.
- Middle-click sets the focus without changing the cursor.
- Right-click opens a context menu either for the alignment pane, for a residue selection or the rubber band selection.
- Dragging creates a mouse selection.
- Dragging over more than one rows creates a rectangular region.
Residue selections and annotations within the rectangle are selected.
Shift-key for union-set and Ctrl-key for cut-set similar to the program gimp or the MS-Window desktop.
- Alt+Drag scrolls two-dimensionally. Under Unix/Linux also hold Shift-key
-
Row-header
- Dragging up/down changes the order of sequences.
- Ctrl+click selects or deselects the sequence.
- Right-click opens a context menu for the sequence.
-
Scroll-bar or alignment pane
- Wheel: Scrolls.
- Shift+Wheel: Scrolls vertically
- Ctrl+Wheel: Zoom.
Sequence groups
G x | Define all currently selected sequences as group "x". |
g x | Load and select sequences of sequence group "x" if not already loaded. Select these sequences. |
h x | Hide all sequences of sequence group "x". |
u x | Unselect all sequences of sequence group "x". |
Sequence Groups:
Sequences can be grouped. Groups are designated by a digit or letter.
The names of all sequences of a group are listed in a file in HTMLDOC_FILE:DIR_SEQUENCE_GROUPS.
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