-\exstep{Close all windows in Jalview and load the ferredoxin alignment (PFAM
-ID PF03460). Choose a residue and place the mouse cursor on it. Click and drag the mouse cursor to create a selection. As you drag, a red box will `rubber band' out to show the extent of the selection. Release the mouse button and a red box should border the selected region. Now press [ESC] to clear the selection.} \exstep{
-Select one sequence by clicking on the ID panel. Note that the sequence ID takes on a highlighted background and a red box appears around the selected sequence. Now hold down [SHIFT] and click another sequence ID a few positions above or below. Note how the selection expands to include all the sequences between the two positions on which you clicked.
-Now hold down [CTRL] and click on several sequences ID's both selected and unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are individually deselected.
-}
-\exstep{ Repeat the step above but selecting columns by clicking on the ruler bar instead of selecting rows by clicking on the sequence ID.
-}
-\exstep{Press [F2] to enter Cursor mode. Navigate to column 59, row 1 by pressing {\sl 5 9 , 1 [RETURN]}. Press {\sl Q} to mark this position. Now navigate to column 65, row 8 by pressing {\sl 6 5 , 8 [RETURN]}. Press {\sl M} to complete the selection.}
-\exstep{\label{exselectgrpcolour}Open the popup menu by right-clicking the
-selected region with the mouse. Open the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour } menu and select `Percentage Identity'. This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences by clicking on their Sequence ID label. Note how the group expands to include newly selected sequences, and the `Percentage Identity' colouring changes. }
-\exstep{
-Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
-
-\exstep{
-Right click on the text area to open the selection popup-menu. Follow the menus and pick an output format from the {\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
-}
-\exstep{Try manually editing the alignment and then press the [New Window] button to import the file into a new alignment window.}
+\exstep{Close all windows in Jalview.
+Load the ferredoxin alignment (PFAM
+ID PF03460 from PFAM seed database).
+Choose a residue and place the mouse
+cursor on it. Note residue information will show in alignment window status bar.
+Click and drag the mouse cursor to create a selection. As you drag, a red box
+will `rubber band' out to
+show the extent of the selection.
+Release the mouse
+button and a red box should border the selected region.
+Press [ESC] to clear the selection.}
+\exstep{ Select one sequence by clicking on
+the sequence ID panel. Note that the sequence ID takes on a highlighted
+background and a red box appears around the selected sequence.
+Hold down [SHIFT] and click another sequence ID a few positions above or below.
+Note how the selection expands to include all the sequences between the two positions on which you clicked.
+
+Hold down [CTRL] and then click on several sequences ID's both selected and
+unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are
+individually deselected.}
+\exstep{ Select column by clicking on the Alignment Ruler. Note whole
+column is highlighted with a red box.
+Hold down [SHIFT] and click column beyond. Note the selection expands to include
+all the sequences between the two positions on which you clicked.}
+
+\exstep{ To selecting arbitrary regions in alignment, place the mouse at the top
+left corner of the region you wish to select. Press and hold the mouse button.
+Drag the mouse to the bottom right corner of the chosen region and release the
+mouse button and a dashed red box appears around the selected region}
+\exstep{Enter Cursor mode using [F2] (or [Fn]-F2 for Macs).
+Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
+Press {\bf Q} to mark this position.
+Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
+to complete the selection. Note to clear the selection press the {\bf[ESC]}
+key.} \exstep{To create a {\bf group} from the selected the region, click the
+right mouse button when mouse is on the selection, this opens the selection
+popup menu in the alignment window.
+
+Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
+} menu and select `Percentage Identity'.
+This will turn the selected region into a group and colour it accordingly.}
+\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
+the alignment by clicking on their Sequence ID label. Note how the group expands
+to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
+
+\exstep{The current selection can be {\bf exported} and saved by right clicking
+on the text area to open the selection popup-menu. Follow the menus and pick an
+output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
+\ldots} submenu.
+}
+\exstep{In the alignment output window, try manually editing the alignment,
+importing group into a new alignment window by clicking the [New Window] button to import the
+file into a new alignment window.}