\vspace{1.2in}
-College of Life Sciences, University of Dundee
+School of Life Sciences, University of Dundee
Dundee, Scotland DD1 5EH, UK
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-9th June 2016
+1st September 2016
\end{center}
$\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
Preview (Mac OS X). Zoom in and note that the image has near-infinite
-resolution.} }
+resolution.}
+}
+
+The next chapters introduce Jalviews analysis features. Chapter \ref{featannot}
+describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation, and how they can be displayed, imported and exported and used to reorder the alignment. Chapter
+\ref{featuresfromdb} discusses the retrieval of database references and
+establishment of sequence coordinate systems for the retrieval and display of
+features from databases and DAS annotation services.
+Chapter \ref{msaservices} describes how to use the range of multiple alignment
+programs provided by JABAWS, and Chapter \ref{aacons} introduces JABAWS AACon
+service for protein multiple alignment conservation analysis.
+ In Chapter \ref{alignanalysis}, you will find
+descriptions and exercises on building and displaying trees, PCA analysis,
+alignment redundancy removal, pairwise alignments and alignment conservation
+analysis.
+Chapter \ref{wkwithstructure} introduces the structure visualization
+capabilities of Jalview.
+Chapter \ref{protsspredservices} explains how to perform protein secondary
+structure predictions with JPred, and JABAWS protein disorder prediction
+services are introduced in Chapter \ref{protdisorderpred}.
+Chapter \ref{workingwithnuc} describes functions and visualization techniques relevant
+to working with nucleotide sequences, coding region annotation and nucleotide
+sequence alignments.
+Chapter \ref{jvwebservices} introduces the various web based services
+available to Jalview users, and Chapter \ref{jabaservices} explains how to
+configure the Jalview Desktop for access to new JABAWS servers.
\chapter{Annotation and Features}
\label{featannot}
-Features and annotations are additional information that is overlaid on the sequences and the alignment. Generally speaking, annotations are associated with columns in the alignment. Features are associated with specific residues in the sequence.
-
-Annotations are shown below the alignment in the annotation panel, and often reflect properties of the alignment as a whole.
+Annotations and features are additional information that is
+overlaid on the sequences and the alignment.
+Generally speaking, annotations reflect properties of the alignment as a
+whole, often associated
+with columns in the alignment. Whilst features are associated with specific residues in the sequence.
+
+Annotations are shown below the alignment in the annotation panel, the
+properties are often based on the alignment.
Conversely, sequence features are properties of the individual sequences, so they do not change with the alignment,
but are shown mapped on to specific residues within the alignment.
\subsection{Creating User Defined Annotation}
-Annotations are properties that apply to the alignment as a whole and are visualized on rows in the annotation panel.
To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}).
A dialogue box appears. Enter the label to use for this row and a new row will appear.
\chapter{Multiple Sequence Alignment}
\label{msaservices}
Sequences can be aligned using a range of algorithms provided by JABA web
-services. These include ClustalW\footnote{{\sl ``CLUSTAL W: improving the
-sensitivity of progressive multiple sequence alignment through sequence
+services, including ClustalW\footnote{{\sl ``CLUSTAL W:
+improving the sensitivity of progressive multiple sequence alignment through sequence
weighting, position specific gap penalties and weight matrix choice."} Thompson
JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic Acids Research} {\bf 22},
4673-80}, Muscle\footnote{{\sl ``MUSCLE: a multiple sequence alignment method
McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) {\sl Molecular
Systems Biology} {\bf 7} 539
\href{http://dx.doi.org/10.1038/msb.2011.75}{doi:10.1038/msb.2011.75}} Of these,
-T-COFFEE is the slowest, but also the most accurate. ClustalW is historically
-the most widely used. Muscle is faster than ClustalW and probably the most
-accurate for smaller alignments and MAFFT is probably the best for large
-alignments, however {\bf Clustal Omega}, which was released in 2011, is
-arguably the fastest and most accurate tool for protein multiple alignment.
-
+T-COFFEE is slow but the accurate. ClustalW is historically
+the most widely used. Muscle is fast and probably best for
+smaller alignments. MAFFT is probably the best for large alignments,
+however Clustal Omega, released in 2011, is arguably the fastest and most
+accurate tool for protein multiple alignment.
To run an alignment web service, select the appropriate method from the {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ \ldots} submenu (Figure
Sort } sub menu.
\subsubsection{Realignment}
-The re-alignment option is currently only supported by ClustalW and Clustal
-Omega. When performing a re-alignment, Jalview submits the current selection to
-the alignment service complete with any existing gaps. This approach is useful
-when one wishes to align additional sequences to an existing alignment without
+The re-alignment option is currently only supported by Clustal
+Omega and ClustalW. When performing a re-alignment, Jalview submits the
+current selection to the alignment service complete with any existing gaps. This
+approach is useful when one wishes to align additional sequences to an existing alignment without
any further optimisation to the existing alignment. The re-alignment service
provided by ClustalW in this case is effectively a simple form of profile
alignment.
-
\begin{figure}[htbp]
\begin{center}
\parbox[c]{1.5in}{\includegraphics[width=1.5in]{images/ws1.pdf}}
\end{center}
\end{figure}
-
-
-
-\exercise{Multiple Sequence Alignment}{
-\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}.
-A window will open giving the job status. After a short time, a second window will open
- with the results of the alignment.}
- \exstep{Return to the first sequence alignment window by clicking on
- the window, and repeat using Clustal and MAFFT (from the {\sl Web
- Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and
- you should notice small differences. }
-\exstep{Select the last three sequences in the MAFFT alignment, and de-align them
-with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect them and then
-submit the view for re-alignment with Clustal.}
-\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment.
-Once the Clustal re-alignment has completed, compare the results of re-alignment of the
-three sequences with their alignment in the original MAFFT result.}
-\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them.
-Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to
-submit the visible portion of the alignment to MAFFT. When the web service job pane appears,
-note that there are now two alignment job status panes shown in the window.}
-\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible
-region in the result with the corresponding region of the original alignment. If you wish,
-select and hide a few more columns in the N-terminal region, and submit the alignment to the
-service again and explore the effect of local alignment on the non-homologous parts of the
-N-terminal region.}
-}
-
\subsubsection{Alignments of Sequences that include Hidden Regions}
-
If the view or selected region that is submitted for alignment contains hidden
regions, then {\bf only the visible sequences will be submitted to the service}.
Furthermore, each contiguous segment of sequences will be aligned independently
\subsection{Customising the Parameters used for Alignment}
-
JABA web services allow you to vary the parameters used when performing a
bioinformatics analysis. For JABA alignment services, this means you are
usually able to modify the following types of parameters:
\item Number of rounds of re-alignment or alignment optimisation
\end{list}
-
\subsubsection{Getting Help on the Parameters for a Service}
Each parameter available for a method usually has a short description, which
Jalview will display as a tooltip, or as a text pane that can be opened under
service can also be accessed, by right clicking the button and selecting a URL
from the pop-up menu that will open.
+\exercise{Multiple Sequence Alignment}{
+\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}.
+A window will open giving the job status. After a short time, a second window will open
+ with the results of the alignment.}
+ \exstep{Return to the first sequence alignment window by clicking on
+ the window, and repeat using ClustalO (Omega) and MAFFT (from the {\sl Web
+ Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and
+ you should notice small differences. }
+\exstep{Select the last three sequences in the MAFFT alignment, and de-align them
+with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
+sequecnes. Then submit this view for re-alignment with ClustalO.}
+\exstep{Return to the window in section (c), use [CTRL]-Z (undo) to recover the
+alignment of the last three sequences in this MAFFT alignment.
+Once the ClustalO re-alignment has completed, compare the results of
+re-alignment of the three sequences with their alignment in the original MAFFT result.}
+\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them,
+by right clicking the mouse to bring up context menu.
+Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to
+submit the visible portion of the alignment to MAFFT. When the web service job pane appears,
+note that there are now two alignment job status panes shown in the window.}
+\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible
+region in the result with the corresponding region of the original alignment.}
+\exstep {If you wish,
+select and hide a few more columns in the N-terminal region, and submit the alignment to the
+service again and explore the effect of local alignment on the non-homologous parts of the
+N-terminal region.}
+}
+
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2.5in]{images/clustalwparamdetail.pdf}
in Jalview's built in documentation.\footnote{See
\url{http://www.jalview.org/help/html/calculations/pca.html}.}
-
-\exercise{Principal Component Analysis}{ \exstep{Load the alignment at
-\textsf{http://www.jalview.org/tutorial/alignment.fa} }
-\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}.
-A new window will open. Move this window so that the tree, alignment and PCA viewer window are all 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 them on the alignment. }
-\exstep{ Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using BLOSUM62}. A new tree window will appear.
-Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups,
-each of a different colour.
-Note how the colour of the sequence ID label matches both the colour of
-the partitioned tree and the points in the PCA plot.} }
-
\subsubsection{The PCA Viewer}
PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principlal
representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
+\exercise{Principal Component Analysis}
+{ \exstep{Load the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa} }
+\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}.
+A new window will open. Move this window so that the tree, alignment and PCA viewer window are all 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 them on the alignment. }
+\exstep{ Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
+Neighbour Joining Using BLOSUM62}. A new tree window will appear.
+Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups,
+each of a different colour.
+Note how the colour of the sequence ID label matches both the colour of
+the partitioned tree and the points in the PCA plot.} }
+
\begin{figure}[hbtp]
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
``Webstart'' column, click on ``G2''.)}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
-\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
-\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring
-makes it easy to see the differences between the two trees, calculated using
+\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour.
+Place the cursor to give about 4 groups. In the alignment window, select
+{\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are
+reordered to match the order in the tree and groups are formed implicitly.
+Alternatively in the tree window, select {\sl View $\Rightarrow$ Sort Alignment
+by Tree}.} \exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree
+$\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the differences between the two trees, calculated using
different methods.} \exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
-Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the alignment for the calculation of trees.
-}
-\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
+Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the
+alignment for the calculation of trees. }}
+
+\exercise{Pad Gaps in Alignment}{
+\exstep{Recover the {\sl Input Data} for the tree you just calculated from the
+{\sl File} menu. In alignment window, ensure that the {\sl Edit $\Rightarrow$
+Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the
+alignment.}
+\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
+Neighbour Joining Using BLOSUM62}.
A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
-\exstep{Now select {\sl Edit $\Rightarrow$ Pad Gaps } and try to perform the tree calculation again - this time a new tree should appear.
+\exstep{Select {\sl Edit $\Rightarrow$ tick Pad Gaps } and perform the
+tree calculation again. This time a new tree should appear - because padding
+gaps ensures all the sequences are the same length after editing.
-This demonstrates the use of the {\sl Pad Gaps } editing preference, which ensures that all sequences are the same length after editing. }
+{\sl Pad Gaps } option
+can also be set using
+{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}. }
}
\exercise{Tree Based Conservation Analysis}{
\label{consanalyexerc}
-\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbour joining tree using BLOSUM62 and use the {\sl Sort
-Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.} \exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
+\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher.
+Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}
+, and set {\sl Conservation } shading threshold at around 20. }
+\exstep{Build a Neighbour joining tree using Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
+Neighbour Joining Using BLOSUM62}.}
+\exstep{Use the mouse cursor to select a point on the tree to partition the
+alignment}
+\exstep {{\sl Sort Alignment By Tree} option in the tree viewer submenu to
+re-order the sequences in the alignment using the calculated tree. Examine the
+variation in colouring between different groups of sequences in the alignment
+window.
You may find it easier to browse the alignment if you first uncheck the {\sl
Annotations $\Rightarrow$ Show Annotations} option, and open the Overview Window
within the View menu to aid navigation.}
-\exstep{Try changing the colourscheme to BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected)}
-{\sl Note: You may want to save the alignment and tree as a project file, since
-it is used in the next few exercises. } }
+
+\exstep{Try changing the colourscheme of the residues in the alignment to
+BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected).}
+{\sl Note: You may want to save the alignment and tree as a project file, since it is used in the next few exercises. } }
\subsection{Redundancy Removal}
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
the alignment window, you may need to deselect groups using Esc key.}
-\exstep{In the Edit menu select Remove Redundancy to open the Redundancy
-threshold selection dialog. Adjust the redundancy threshold value, start
+
+\exstep{In the {\sl Edit} menu select {\sl Remove Redundancy} to open the
+Redundancy threshold selection dialog. Adjust the redundancy threshold value, start
at 50 and increase the value to 65. Sequences selected will change colour in the Sequence ID panel. Select ``Remove'' to
remove the sequences that are more than 65\% similar under this alignment.}
+
\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
\exstep{Use the [Undo] button in the Redundancy threshold selection dialog box
to recover the sequences. Note that the * symbols disappear from the tree display.}
\exercise{Group Conservation Analysis}{
\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 View menu, create a new view. Ensure the annotation panel
-is displayed (Show annotation in Annotations menu). Enable the display
-of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
-Autocalculated Annotation } submenu in the sequence alignment window. Then display of sequence
-logos to make it easier to see the different residue populations within each
-group. Activate logo by right clicking on the Consensus annotation row to open
-the pop-up menu and select the {\sl Show Logo} option.}
+\exstep{In the {\sl View} menu, select {\sl New View} to create a new
+view. Ensure the annotation panel is displayed ({\sl Show annotation} in {\sl Annotations} menu). Enable the
+display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
+Autocalculated Annotation } submenu in the sequence alignment window.}
+\exstep{Displaying the sequence
+logos will make it easier to see the different residue populations within each
+group. Activate the logo by right clicking on the Consensus annotation row to
+open the context menu and select the {\sl Show Logo} option.}
\exstep{In the column alignment ruler, select a column exhibiting about 50\%
-conservation that lies within the central conserved region of the alignment. Subdivide the alignment according to
-this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
+conservation that lies within the central conserved region of the alignment.
+(Column 74 is used in the Tree video).}
+\exstep{Subdivide the alignment
+according to this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
\exstep{Re-order the alignment according to the new groups that have been
-defined. Click on the group annotation row IDs to select groups exhibiting a
+defined by selecting {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
+By Group}.
+
+Click on the group annotation row IDs to select groups exhibiting a
specific mutation.}
\exstep{Select another column exhibiting about 50\% conservation
overall, and subdivide the alignment further. Note that the new groups
\chapter{Working with 3D structures}
\label{3Dstructure}
+Jalview can interactively view 3D structure using Jmol or Chimera. Setting in
+the Structure window within Preferences determine whether Jmol or Chimera is
+the default choice of structure viewer.
+
+% To review, Chapter \ref{featannot} describes the mechanisms provided by
+% Jalview for interactive creation of sequence and alignment annotation, and how
+% they can be displayed, imported and exported and used to reorder the alignment. Chapter
+% \ref{featuresfromdb} discusses the retrieval of database references and
+% establishment of sequence coordinate systems for the retrieval and display of
+% features from databases and DAS annotation services.
+% Chapter \ref{msaservices} describes how to use the range of multiple alignment
+% programs provided by JABAWS, and Chapter \ref{aacons} introduces JABAWS AACon
+% service for protein multiple alignment conservation analysis.
+% In Chapter \ref{alignanalysis}, you will find
+% descriptions and exercises on building and displaying trees, PCA analysis,
+% alignment redundancy removal, pairwise alignments and alignment conservation
+% analysis.
+% Chapter \ref{wkwithstructure} introduces the structure visualization
+% capabilities of Jalview.
+% Chapter \ref{protsspredservices} explains how to perform protein secondary
+% structure predictions with JPred, and JABAWS protein disorder prediction
+% services are introduced in Chapter \ref{protdisorderpred}.
+% Chapter \ref{workingwithnuc} describes functions and visualization techniques
+% relevant to working with nucleotide sequences, coding region annotation and nucleotide
+% sequence alignments.
+% Chapter \ref{jvwebservices} introduces the various web based services
+% available to Jalview users, and Chapter \ref{jabaservices} explains how to
+% configure the Jalview Desktop for access to new JABAWS servers.
-To summarise, section \ref{featannot} describes the mechanisms provided by
-Jalview for interactive creation of sequence and alignment annotation, and how they can be
-displayed, imported and exported and used to reorder the alignment. Section
-\ref{featuresfromdb} discusses the retrieval of database references and
-establishment of sequence coordinate systems for the retrieval and display of
-features from databases and DAS annotation services.
-Section \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS AACon
-service for protein multiple alignment conservation analysis.
- In Section \ref{alignanalysis}, you will find
-descriptions and exercises on building and displaying trees, PCA analysis,
-alignment redundancy removal, pairwise alignments and alignment conservation
-analysis.
-Section \ref{wkwithstructure} introduces the structure visualization
-capabilities of Jalview.
-Section \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS protein disorder prediction
-services are introduced in Section \ref{protdisorderpred}.
-Section \ref{workingwithnuc} describes functions and visualization techniques relevant
-to working with nucleotide sequences, coding region annotation and nucleotide
-sequence alignments.
-Section \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Section \ref{jabaservices} explains how to
-configure the Jalview Desktop for access to new JABAWS servers.
-
-
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
automatic application of colour schemes when new structure data is added, or
when associated alignment views are modified.
-
-\exercise{Viewing Structures}{\label{viewingstructex}
+\exercise{Viewing Structures in Jmol viewer}{\label{viewingstructex}
\exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the
-sequence ID label of {\sl FER1\_SPIOL}, this brings up
-the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
-Associate Structure with Sequence $\Rightarrow$ Discover
-PDB IDs}. Jalview will now attempt to find PDB structures for the sequences in
-the alignment.
+\textsf{http://www.jalview.org/examples/exampleFile.jar}.}
+\exstep{Right-click on the
+sequence ID label of {\sl FER1\_SPIOL} to open
+the context menu. Select {\sl 3D Structure}, this
+opens a Structure Chooser window, select { \sl 1A70} and click { ok}.
+
+{\sl Note: the Structure Chooser interface
+provides a smart technique for selecting PDB structures by queryingthe meta-data
+of structures. Extra information can be including in this window by checking boxes
+in the ``Configure Displayed Columns'' tab}.
% JBP Note: Bug JAL-1238 needs to be fixed ASAP
-
-{\bf Note:} If you are using Jalview v2.8 - use the {\sl Uniprot } source from the {\sl Web services $\Rightarrow$ Fetch DB References $\Rightarrow$ ..} submenu of the Alignment Window to retrieve the PDB IDs. }
-\exstep{ Right-click on the sequence ID for {\sl FER1\_SPIOL}.
-Select { \sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$ View Structure
-$\Rightarrow$ 1A70}. A structure viewing window appears. Rotate the molecule by clicking and dragging in the structure viewing box. Zoom with the mouse scroll wheel. } \exstep{Roll the mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment. Note that if a residue in the sequence maps to one in the structure, a label will appear next to that residue in the structure viewer. Move the mouse over the structure. Placing the mouse over a part of the structure will bring up a tool tip indicating the name and number of that residue. The corresponding residue in the sequence is highlighted in black. Clicking the alpha carbon toggles the highlight and residue label on and off. Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
-\exstep{Select {\sl Colours $\Rightarrow$ Background Colour\ldots} from the structure viewer menu and choose a suitable colour. Press OK to apply this. Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the image. View this with a suitable program. }
-\exstep{Select {\sl File $\Rightarrow$ View Mapping} from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.}
-\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file. Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
-
-\exstep{Right click on the structure in the submenu and bring up the Jmol
-window.
-Explore the menu options. Try to change the style of molecular display - by first using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.} \exstep{Use the {\sl File $\Rightarrow$ Save As .. } function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
-
-Verify that the Jmol display is as it was when you just saved the file.}
}
+\exstep{By default the Jmol
+structure viewer opens in the Jalview desktop. Rotate the molecule by clicking
+and dragging in the structure viewing box.
+Zoom with the mouse scroll wheel. }
+\exstep{Roll the
+mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment.
+Note that if a residue in the sequence maps to one in the structure, a label
+will appear next to that residue in the structure viewer.}
+\exstep{Move the mouse over the structure. In the Jmol viewer, placing the mouse over a
+part of the structure will bring up a tool tip indicating the name and number of that residue.
+In the alignment window, the corresponding residue in the sequence is
+highlighted in black.}
+\exstep{Clicking the alpha carbon toggles the highlight and residue label on and
+off.
+Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
+\exstep{In the structure viewer menu, select {\sl Colours $\Rightarrow$ Background
+Colour\ldots} and choose a suitable colour.
+Press OK to apply this.}
+\exstep{Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the
+image. On your computer, view this with a suitable program. }
+\exstep{Select
+{\sl File $\Rightarrow$ View Mapping} from the structure viewer menu.
+A new window opens showing the residue by residue alignment between the sequence and the structure.}
+\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file.
+Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on
+to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu).
+Verify that you can open and view the associated structure from the sequence ID
+pop-up menu's {\sl 3D Structure } submenu in the new alignment window.}
+
+\exstep{In the Jmol window, right click on the structure window and explore the
+menu options. Try to change the style of molecular display - for example by
+using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.}
+\exstep{In the alignment window, use the {\sl File $\Rightarrow$ Save As .. }
+function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
+Verify that the Jmol display is as it was when you just saved the file.}}
+
+\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.
+
+\exstep{First, Chimera must be downloaded and installed on the computer.
+Chimera program is available on the UCSF web site \textsf{https://www.cgl.ucsf.edu/chimera/download.html}.}
+\exstep{In the desktop menu, select {\sl Tool $\Rightarrow$ Preferences}. In
+the ``{\sl
+Structure}'' tab set {\sl Default structure viewer} as {\sl
+Chimera}; then click {\sl OK}.}
+\exstep{Close the Jalview program, from the
+{\sl Desktop menu} select {\sl Jalview $\Rightarrow$ Quit Jalview}. Then reopen
+Jalview, Chimera should open as the default viewer.}
+{\s Note: The Jmol structure viewer sits within the Jalview desktop; however the Chimera structure viewer
+sits outside the Jalview desktop and a Chimera
+view window sits inside the Jalview desktop.} }
\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}
\end{center}
\end{figure}
-\exercise{Aligning Structures using the Ferredoxin
-Sequence Alignment}{\label{superpositionex}
-
-\exstep{Continue with the Jalview project created in exercise
-\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
-IDs associated with the FER1\_MAIZE sequence.}
-\exstep{Once discovery has completed, use the {\sl
-View PDB Structure} submenu to view one of the PDB file associated with
-FER1\_MAIZE (eg. 3B2F)
-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 the {\bf Yes} button.
-
-{\sl The Jmol view will 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.}
-\exstep{Use the {\sl Jmol} submenu to
-recompute the superposition using just columns 121-132 of the alignment
-(The easiest way to achieve this is to select column 121-132 and in the View
-menu selected ``All but selected region'' from the Hide options).
-
-{\sl Note how the molecules shift position when superposed using a short part of
-the two structures.}}
-\exstep{Compare the initial and final RMSDs for superimposing molecules with
-the small section and with the whole alignment. (The RMSD report can be
-viewed by right clicking the mouse on Jmol window, and select ``Show" and ``Measurements") Which view do you think give the best 3D
-superposition, and why ?} }
-
\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
\end{center}
\end{figure}
+\exercise{Aligning Structures using the Ferredoxin
+Sequence Alignment}{\label{superpositionex}
+
+\exstep{Continue with the Jalview project created in exercise
+\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
+IDs associated with the FER1\_MAIZE sequence.}
+\exstep{Once discovery has completed, use the {\sl
+View PDB Structure} submenu to view one of the PDB file associated with
+FER1\_MAIZE (eg. 3B2F)
+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 the {\bf Yes} button.
+
+{\sl The Jmol view will 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.}
+\exstep{Use the {\sl Jmol} submenu to
+recompute the superposition using just columns 121-132 of the alignment
+(The easiest way to achieve this is to select column 121-132 and in the View
+menu selected ``All but selected region'' from the Hide options).
+
+{\sl Note how the molecules shift position when superposed using a short part of
+the two structures.}}
+\exstep{Compare the initial and final RMSDs for superimposing molecules with
+the small section and with the whole alignment. (The RMSD report can be
+viewed by right clicking the mouse on Jmol window, and select ``Show" and ``Measurements") Which view do you think give the best 3D
+superposition, and why ?} }
+
\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
The ability to control which multiple alignment view is used to colour
This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
server.}
-
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
free memory available.
-
{\sl Use the following webstart link:
-
\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}
-
{\sl Alternatively in the Development section of the Jalview web site
(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
in the ``latest official build'' row in the table, go to the
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
-\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear. Note that the number of sequences in the results window is many more than in the original alignment as JNet performs a PSI-BLAST search to expand the prediction dataset.
-}
+\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by
+clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction}
+from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear.
+Note that the number of sequences in the results window is many more than in the original alignment as
+JNet performs a PSI-BLAST search to expand the prediction dataset. The results
+from the prediction are visible in the annotation panel. Jnet secondary
+structure prediction annotations are examples of sequence-associated alignment annotation. }
% TODO: check how long this takes - about 2 mins once it gets on the cluster.
\exstep{
Select a different sequence and perform a JNet prediction in the same way. There will probably be minor differences in the predictions.
}
\exstep{
-Select the second sequence prediction, and copy and paste it into the first
-prediction window. You can now compare the two predictions. Jnet secondary structure prediction annotations are examples of {\bf sequence-associated alignment annotation}.
+Select the sequence used in the second sequence prediction by clicking on its
+name in the sequence ID panel, and copy {\sl (CTRL or Command + C)} and then
+paste it {\sl (CTRL or Command + V)} into the first prediction window. You
+can now compare the two predictions as the annotations associated with the
+sequence has also been copied across.
% which is described in Section \ref{seqassocannot} below.
}
\exstep{
-Select and hide some columns in one of the profiles that were returned from the JNet service, and then submit the profile for prediction again.
+Select and hide some columns in one of the alignment profiles that were returned
+from the JNet service, and then submit the profile for prediction again.
}
\exstep{
When you get the result, verify that the prediction has not been made for the
-hidden parts of the profile, and that the JPred reliability scores differ from the prediction made on the full profile.
-
-{\sl Note: you may want to keep this data for use in exercise \ref{viewannotfileex}.}
+hidden parts of the profile (by clicking the mouse on column ruler and right click to open the
+context menu and select {\sl Reveal All}), and that the JPred reliability scores
+differ from the prediction made on the full profile.
}
\exstep{
-In the original alignment that you loaded in step 1, {\bf select all} sequences,
-then open the {\bf Sequence ID $\Rightarrow$ Selection } submenu and select the
-{\bf Add Reference Annotation} option.
-
-The JNet predictions for the sequences should now be visible in the original
-alignment.} }
+In the original alignment that you loaded in step 1, select {\bf all}
+sequences, then open the {\sl Sequence ID $\Rightarrow$ Selection } submenu
+by right clicking the mouse to open the context menu, and select the {\sl Add
+Reference Annotation} option.
+
+{\bf All} the JNet predictions for the sequences will now be visible in the
+original alignment window.
+
+{\sl Note: The annotation panel can get quite busy and it may be
+helpful to hide some of the annotations rows, by right clicking the mouse in
+the annotation label panel and select ``Hide this row'' option in the context
+menu}.} }
\begin{figure}[htbp]
\begin{center}
git://source.jalview.org / jalview-manual.git / commitdiff