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JAL-3111 patch exercises for revised Structure Viewer dialog
author
Jim Procter
<jprocter@issues.jalview.org>
Wed, 8 May 2019 14:35:21 +0000
(15:35 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Wed, 8 May 2019 14:35:21 +0000
(15:35 +0100)
TheJalviewTutorial.tex
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diff --git
a/TheJalviewTutorial.tex
b/TheJalviewTutorial.tex
index
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9097dc0
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--- 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{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 } }
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.
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
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
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
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
\exstep{Pick a different
colourscheme for each alignment, and use the {\sl Colour by ..} submenu to