From: Jim Procter Date: Mon, 14 Jun 2010 09:10:58 +0000 (+0000) Subject: spellchecking X-Git-Tag: Version_1.9.2~92 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=ca68eaae0757957a72110d02c097642cb6f76662 spellchecking --- diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 52faea0..496d6fe 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -462,7 +462,7 @@ From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save \exercise{Saving Alignments}{ \label{save} -\exstep{Start Jalview, close all windows and load the ferrodoxin alignment from pFam (accession number PF03460 (see Exercise \ref{load}). +\exstep{Start Jalview, close all windows and load the ferredoxin alignment from pFam (accession number PF03460 (see Exercise \ref{load}). } \exstep{ Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a location into which to save the alignment and select a format. All formats except {\sl Jalview } can be viewed in a normal text editor (e.g. Notepad) or in a web browser. Enter a file name and click {\sl Save}. Check this file by browsing to it with your web browser or by closing all windows and opening it with Jalview. @@ -566,8 +566,8 @@ The current selection can be copied to the system clipboard (in PFAM format). It \exercise{Making selections and groups}{ \label{exselect} -\exstep{Close all windows in Jalview and load the ferrodoxin 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{ +\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. } @@ -714,7 +714,7 @@ group is dragged to the right with [CTRL] pressed.} \label{mousealedit} \exstep{ Load the URL \textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the -ferrodoxin alignment from PF03460. +ferredoxin alignment from PF03460. You are going to manually reconstruct the alignment that jalview loads by default. Remember to use [CTRL]+Z to undo an edit, or the {\tr File $\LeftArrow$ @@ -740,7 +740,7 @@ sequences at column 38 by holding [CTRL] and clicking on the R in FER1\_SPIOL an dragging one column to right. Insert another gap at column 47 in all sequences in the same way.} -\exstep{ Correct the feredoxin domain alignment for FER1\_SPIOL by +\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by insert two additional gaps after the gap at column 47: hold [SHIFT] and click and drag on the G and move it two columns to the right.} diff --git a/latest/TheJalviewTutorial.pdf b/latest/TheJalviewTutorial.pdf index 26e05a0..3f19241 100644 Binary files a/latest/TheJalviewTutorial.pdf and b/latest/TheJalviewTutorial.pdf differ diff --git a/latest/TheJalviewTutorial_screen.pdf b/latest/TheJalviewTutorial_screen.pdf index 7db1ab8..07c0809 100644 Binary files a/latest/TheJalviewTutorial_screen.pdf and b/latest/TheJalviewTutorial_screen.pdf differ