From: Jim Procter Date: Wed, 8 May 2019 14:35:21 +0000 (+0100) Subject: JAL-3111 patch exercises for revised Structure Viewer dialog X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=173a69130cc3ade8c28e41fa2879d4d0a3b4e448;p=jalview-manual.git JAL-3111 patch exercises for revised Structure Viewer dialog --- diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 46ca917..9097dc0 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -3273,11 +3273,11 @@ Verify that the Jmol display is as it was when you just saved the file.} \exstep{Continue with the Jalview project created in exercise \ref{viewingstructex}} -\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL +\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_MAIZE by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$ 3D Structure Data \ldots } } -\exstep{Pick 1A70 from the Structure Chooser dialog, and make sure the {\sl Superimpose} option is checked before clicking the {\bf Add} +\exstep{Pick 1gaq from the Structure Chooser dialog, and make sure the {\sl Superpose} option is checked before clicking the {\bf Add} button to superimpose the structure associated with FER1\_MAIZE with the one associated with FER1\_SPIOL. @@ -3477,7 +3477,7 @@ each one, open the Structure Chooser dialog box by right clicking the mouse on sequence name to open the context menu and select {\sl $\Rightarrow$ 3D Structure Data}. Select `Cached Structures' from -the drop-down menu in the Structure Chooser dialog box, select the +the drop-down menu in the Structure Chooser dialog box and select the DNMT1\_MOUSE.pdb structure, and click {\bf View}. {\em Part of the newly opened structure will be coloured the same way as @@ -3488,10 +3488,9 @@ the associated DNMT1\_MOUSE sequence is in the alignment view.} sequences in the alignment.} } \exstep{Repeat the previous two steps for each of the other -alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and -hitting the `View' button on the Structure Chooser dialog. Jalview will ask if -you wish to create a new Jmol view, respond {\bf `Yes'} each time. This will -ensure each sequence fragment is associated with the {\bf same} Jmol view. } + alignments. For those, after selecting the DNMT1\_MOUSE.pdb structure you + should select `Add' to ensure each domain alignment is associated + with the {\bf same} Jmol view. } \exstep{Pick a different colourscheme for each alignment, and use the {\sl Colour by ..} submenu to