% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-10th November 2017
+17th November 2017
\end{center}
\exstep{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
the URL history button (a downward arrow on the right hand side of the dialog
-box) to view the files, select exampleFile\_2\_7.jar, then click {\sl OK}.}
-{\bf Note:} Should you want to load your own
-sequence during the launch process, then go
+box) to view the files, select exampleFile\_2\_7.jar
+(\url{http://www.jalview.org/examples/exampleFile_2_3.jar})
+then click {\sl OK}.}
+{\bf Note:} Should you want to load your own sequence during the launch process, then go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
preferences tab, type in the URL of the sequence you want to load.
%TODO insert a figure for the Find dialog box
\exercise{Navigation}{
+\label{navigationEx}
Jalview has two navigation and editing modes: {\bf normal} mode (where editing
and navigation are via the mouse) and the {\bf cursor} mode (where editing and
navigation are via the keyboard).
suitable folder.}
\exstep{Close all windows and then load the project {\sl via} the {\sl File
-$\Rightarrow$ Load Project} menu option. Observe how many of the windows are as they were when they were saved. }
-{\bf See the video at: \url{http://www.jalview.org/Help/Getting-Started}.}
-}
+$\Rightarrow$ Load Project} menu option. Observe how many of the windows
+reopen. Are they the same as were saved. } {\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}.} }
\chapter{Selecting and Editing Sequences }
\end{figure}
\exercise{Reordering the Alignment}{
+\label{reorderex}
\exstep{Close windows.
Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
sequence group.
\exercise{Hiding and Revealing Regions}{
+\label{hidingex}
\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
}
\exstep{Select a contiguous set of sequences by clicking and dragging on the sequence ID panel.
\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
-{You are going to manually reconstruct part of the example Jalview
+{
+\label{editingalignex}
+You are going to manually reconstruct part of the example Jalview
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
\exercise{Keyboard Edits}
-{This continues on from the previous exercise, and recreates the final part of the example ferredoxin
+{
+\label{keyboardsex}
+This continues on from the previous exercise, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
{\bf Window users:} Please {\em only use} [SHIFT]-[SPACE] in this
\exercise{User Defined Colour Schemes}{
-\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialog window will open.}
+\label{colouex}
+\exstep{Load a sequence alignment. Ensure that the {\sl Colour $\Rightarrow$
+None} is selected. Select the alignment menu option {\sl Colour $\Rightarrow$
+User Defined}.
+A dialog window will open.}
\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.}
\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialog window can now be closed.}
\exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
annotation row labels to bring up the context menu, then select {\sl
Hide This Row}. Bring up the context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
-\exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just
-above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
+\exstep{Annotations can be reordered by clicking on the sequence name and
+dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
\exstep{Move the mouse to the top left hand corner of the annotation labels -
a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
by clicking and dragging this icon up or down.}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
\exercise{Graphical Output}{
+ \label{graphicex}
\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}.
Customise it how you wish but leave it unwrapped.
Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu.
\exercise{Annotating Alignments}{
\label{annotatingalignex}
\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
-Right-click on the {\sl Conservation} annotation row to
+Right-click on the label name of the {\sl Conservation} annotation row to
bring up the context menu and select {\sl Add New Row}. A dialog box will
appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
and find the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents
pane.) }
-\exstep{Export the file to a text editor and edit the file to change the name of the annotation
-row. Save the file and drag it onto the alignment view.}
-\exstep{Add an additional helix somewhere along the row by editing the file and
-re-importing it.
-
+\exstep{Open a text editor and copy the annotation text into the editor.
+Edit the text by changing the name of the annotation row and save the file.}
+\exstep{Drag the file onto the alignment in Jalview and check the annotation
+panel.} \exstep{Return to the text editor, add an additional helix somewhere
+along the row, save the file and re-importing it into Jalview as previously.
{\sl Hint: Use the Export Annotation function to view what helix annotation looks like in
a Jalview annotation file.}}
\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
-function to export all the alignment's annotation to a file.}
+function to export all the alignment's annotation to a file. Save the file.}
\exstep{Open the exported annotation in a text editor, and use the Annotation File Format
documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
they appear as several lines on a single line graph.
-
{\sl Hint: You need to change the style of annotation row in the first field of the annotation
-row entry in the file, and create an annotation row grouping to overlay the three quantitative
-annotation rows.}
+row entry in the file. Create an annotation row grouping to overlay the
+three quantitative annotation rows.}
}
-\exstep{{\bf Homework for after you have completed exercise \ref{secstrpredex}:}
+\exstep{{\bf Homework once you have completed exercise
+\ref{secstrpredex}:}
\label{viewannotfileex}
Recover or recreate the secondary structure predictions that you made from
JPred. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row.
-Note the
+Note: the
SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
annotation.
}
features file.
\exercise{Creating Features}{
+\label{featuresex}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in
iron binding so we will create them as features. Navigate to column 97, sequence 1.
number allowed by the server.
\exercise{Multiple Sequence Alignment}{
+\label{msaex}
\exstep{ Close all windows and open the alignment at {\sf
http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}.
the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
\exercise{Principal Component Analysis}
-{ \exstep{Load the alignment at
+{\label{pcaex}
+\exstep{Load the alignment at
\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
window and a dialogue box will open. Select the Principal Component Analysis option
this window within the desktop so that the alignment and PCA viewer windows are visible.
Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window.
Note that clicking on points in the plot will highlight the sequences on the
-alignment.
-} \exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
-window. In dialogue box select Neighbour
+alignment.}
+\exstep{Use the [ESC] key to deselect sequence selection.
+Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment window. In dialogue box select Neighbour
Joining and in the drop-down list select BLOSUM62. Click the Calculate button
and a tree window will open.}
\exstep{Place the mouse cursor on the tree so that the
{\sl View $\Rightarrow$ Mark Unlinked Leaves} menu option.
\exercise{Trees}
-{{\sl Ensure that you have at least 1G memory available in Jalview.
+{\label{treeex}
+{\sl Ensure that you have at least 1G memory available in Jalview.
(Start with link:
\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
or in the table in the Development section of the Jalview web site
\exercise{Remove Redundant Sequences}{
-
+\label{redundantex}
\exstep{Using the alignment generated in the previous exercise (exercise
\ref{consanalyexerc}).
In the alignment window, you may need to deselect groups using Esc key.}
}
\exercise{Group Conservation Analysis}{
+\label{conservationex}
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc}).}
\exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to
automatic application of colour schemes when new structure data is added, or
when associated alignment views are modified.
-\exercise{Viewing Structures with the integrated Jmol
-Viewer}{\label{viewingstructex} \exstep{Load the alignment at
+\exercise{Viewing Structures with the integrated Jmol Viewer}{
+\label{viewingstructex}
+\exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar}.}
\exstep{Right-click on the
sequence ID label of {\sl FER1\_SPIOL} to open
\url{http://www.jalview.org/training/Training-Videos}.}
}
-\exercise{Setting Chimera as the default 3D Structure Viewer}{\label{viewingchimera}
+\exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{
+\label{superpositionex}
+
+\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
+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 click the {\bf View}
+button. Jalview will give you the option of aligning the
+structure to the one already open. To superimpose the structure associated with
+FER1\_MAIZE with the one associated with FER1\_SPIOL, press {\sl Yes}.
+
+{\sl The Jmol view should update to show both structures, and one will be
+moved on to the other. If this doesn't happen, use the Align function in the
+Jmol submenu}.
+}
+
+\exstep{Create a new view on the alignment, and hide all but columns 121
+through to 132 (you can do this via {\sl View $\Rightarrow$ Hide $\Rightarrow$
+All but selected region}).}
+\exstep{Select the newly created view in the {\sl Jmol $\Rightarrow$ Superpose
+With } submenu, and then recompute the superposition with {\sl Jmol
+$\Rightarrow$ Align Structures}.
+
+{\sl Note how the molecules shift position when superposed with only a small
+region of the alignment.}}
+
+\exstep{Compare RMSDs obtained when superimposing molecules with
+columns 121-132 and with the whole alignment.}
+
+\exstep{The RMSD report can be
+viewed by right clicking the mouse on Jmol window, and select {\sl
+Console} from the menu (if nothing is shown, recompute the superposition after
+displaying the console).
+
+Which view do you think give the best 3D superposition, and why ?} }
+
+\exercise{Setting Chimera as the default 3D Structure Viewer}{
+\label{viewingchimera}
Jalview supports molecular structure
visualization using both Jmol and Chimera 3D viewers. Jmol is the default
viewer, however Chimera can be set up as the default choice from Preferences.
the Chimera structure viewer sits outside the Jalview desktop and a Chimera
view window sits inside the Jalview desktop.}
-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.} }
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}}
+
\subsection{Superimposing Structures}
\label{superposestructs}
Note that these menu options appear when you have two or more structures in one Jmol viewer.
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
-\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
-left was used by Jalview to superpose structures associated with the
-FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
-used for superposition are rendered as a cartoon, the remainder rendered in
-wireframe. The RMSD between corresponding positions in the structures before and
-after the superposition is shown in the Jmol console.}
-\label{mstrucsuperposition}
-\end{center}
-\end{figure}
-
\subsection{Colouring Structure Data Associated with Multiple Alignments and
Views} Normally, the original view from which a particular structure view was
opened will be the one used to colour structure data. If alignments involving
views that colour different areas or domains of the alignment. This option is
further explored in exercise \ref{complexstructurecolours}.
-
-\exercise{Aligning Structures using the Ferredoxin
-Sequence Alignment}{\label{superpositionex}
-
-\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
-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 click the {\bf View}
-button. Jalview will give you the option of aligning the
-structure to the one already open. To superimpose the structure associated with
-FER1\_MAIZE with the one associated with FER1\_SPIOL, press {\sl Yes}.
-
-{\sl The Jmol view should update to show both structures, and one will be
-moved on to the other. If this doesn't happen, use the Align function in the
-Jmol submenu}.
-}
-
-\exstep{Create a new view on the alignment, and hide all but columns 121
-through to 132 (you can do this via {\sl View $\Rightarrow$ Hide $\Rightarrow$
-All but selected region}).}
-\exstep{Select the newly created view in the {\sl Jmol $\Rightarrow$ Superpose
-With } submenu, and then recompute the superposition with {\sl Jmol
-$\Rightarrow$ Align Structures}.
-
-{\sl Note how the molecules shift position when superposed with only a small
-region of the alignment.}}
-
-\exstep{Compare RMSDs obtained when superimposing molecules with
-columns 121-132 and with the whole alignment.}
-
-\exstep{The RMSD report can be
-viewed by right clicking the mouse on Jmol window, and select {\sl
-Console} from the menu (if nothing is shown, recompute the superposition after
-displaying the console).
-
-Which view do you think give the best 3D superposition, and why ?} }
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
+\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
+left was used by Jalview to superpose structures associated with the
+FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
+used for superposition are rendered as a cartoon, the remainder rendered in
+wireframe. The RMSD between corresponding positions in the structures before and
+after the superposition is shown in the Jmol console.}
+\label{mstrucsuperposition}
+\end{center}
+\end{figure}
\begin{figure}[htbp]
\begin{center}
server.}
\exstep{Launch the Jalview desktop and ensure you have at least 1G of
free memory available.
-
{\sl See section \ref{memorylimits} for how to do this or click the following
link:
\exstep{Retrieve the following PFAM alignments from the {\bf PFAM (full)} source
:
+
PF02008 PF01426 PF00145 (enter all three - they
will each be retrieved into their own alignment window).}
\exstep{Drag the URL or file of the structure you
downloaded in step 1 onto one of the alignments to associate it with the mouse sequence in that Pfam domain family.}
-\exstep{Use the Find dialog to locate every DNMT1\_MOUSE sequence in the
-alignment and for each one, open the Structure Chooser via the ID popup
-menu ({\sl $\Rightarrow$ 3D Structure Data }. Select the DNMT1\_MOUSE.pdb
-structure from the `Cached Structures' view, and click {\bf View}.
+\exstep{Locate every DNMT1\_MOUSE sequence in the
+alignment by opening the Find dialog box via {\sl Select
+$\Rightarrow$ Find}. Search using the text DNMT1\_MOUSE. For
+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
+DNMT1\_MOUSE.pdb structure, and click {\bf View}.
{\em Part of the newly opened structure will be coloured the same way as
the associated DNMT1\_MOUSE sequence is in the alignment view.}
}
\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. }
+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. }
\exstep{Pick a different
colourscheme for each alignment, and use the {\sl Colour by ..} submenu to
{\sl Examine the regions strongly coloured at the interfaces between each
protein domain, and the DNA binding region. What do you think these patterns
-mean ? } }
+mean? } }
\exstep{Save your work as a Jalview project and verify that it can be opened
again by starting another Jalview Desktop instance, and dragging the saved
-project into the desktop window.}
+project into the Desktop window.}
% {\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
% you notice any strange behaviour when trying out this exercise, it may be a
annotation panel and selecting \textbf{Show hidden annotation}.
\exercise{Protein Disorder Prediction}{
-%\label{protdispredex}
+\label{protdisorderex}
{\sl Before starting this exercise, make sure you enable the \protect{`Add
Temperature Factor'} option in your {\bf Structures} preferences. }
-\exstep{Open the alignment at:
+\exstep{Open the alignment using
\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
-\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Service
+\exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
$\Rightarrow$ Disorder Prediction } submenu.}
-\exstep{Select all the sequences, and open the Structure Chooser via the {\sl
-Sequence ID $\Rightarrow$ 3D Structure Data\ldots } popup menu. Hit the
-{\bf View} button to retrieve and show all PDB structures for the sequences.}
+\exstep{Select all the sequences. Open the Structure Chooser by placing
+the mouse in the Sequence ID panel, right clicking the mouse and select
+{\sl$\Rightarrow$ 3D Structure Data\ldots }. Select all structures in the list.
+Hit the View button to retrieve and show all PDB structures for the sequences.}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
-\exstep{Apply the IUPred disorder prediction method. Use the {\sl Per
-sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
-the sequences by the long and short disorder predictors. {\sl Note how well the disordered regions predicted by each method agree
+\exstep{Features on sequences can conceal other colouring. This can be
+toggled off by selecting {\sl View
+$\Rightarrow$ Show Sequence Features}.}
+\exstep{Apply the IUPred disorder prediction method. Tick the
+the {\sl Per sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog
+box. Then shade the sequences by the long and short disorder predictors. {\sl
+Note how well the disordered regions predicted by each method agree
with the structure.}}
\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
\exercise{Visualizing Protein Features on Coding Regions}
{
+\label{protfeatureex}
\exstep{Use the sequence fetcher to retrieve ENA record D49489.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the
alignment view format to {\sl Wrapped} mode so the distinct exons can be seen.}
git://source.jalview.org / jalview-manual.git / commitdiff