\subsection{Viewing Structures}
\label{viewAllStructures}
-The structure viewer can be launched in two ways from the sequence ID context
+The structure viewer is launched from the sequence ID context
menu. To view a particular structure associated with a sequence in the
-alignment, simply select it from popup menu's associated structures submenu in
-{\sl Structure $\Rightarrow$ View Structure $\Rightarrow$ $<$PDB ID$>$}. The
-second way is most useful if you want to view all structural data available for
-a set of sequences in an alignment. If any of the {\bf currently selected}
-sequences have structures associated, the {\sl Structure } submenu of the
-sequence ID popup menu will include an option to {\sl View {\bf N}
-structures}. Selecting this option will open a new structure view containing
+alignment, select the sequence and right click the mouse to open context
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} opens a Structure Chooser dialogue box.
+The second way is most useful if you want to view all structural data available for
+a set of sequences in an alignment. Select all the sequence ids in the sequence
+ID panel and right click the mouse to open context
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$}. If any of
+the {\bf currently selected} sequences have structures associated they will
+appear in the Structure Chooser dialogue box. The structures can be ranked by
+different parameters, 'Best Quality' is defaul option. Select the
+structures required and click {\sl View} to open a structure viewer containing
the associated structures superposed according to the alignment.
-In both cases, each structure to be displayed will be downloaded or loaded from
+The structure to be displayed will be downloaded or loaded from
the local file system, and shown as a ribbon diagram coloured according to the
associated sequence in the current alignment view (Figure \ref{structure}
(right)). The structure can be rotated by clicking and dragging in the structure
Jalview can employ Jmol's 3D fitting routines\footnote{See
\href{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}
for more information.} to recreate 3D structure superpositions based on the
-correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view happens automatically if a
-structure is added to an existing Jmol display using the {\sl Structure
-$\Rightarrow$ View PDB Structure $\Rightarrow$ ..}. A new Jmol view containing
-superposed structures can also be created using the {\sl Structure
-$\Rightarrow$ View all {\bf N} PDB Structures} option (when {\bf {\sl N}}
-$>$ 1) if the current selection contains two or more sequences with associated
+correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view
+ happens automatically if a
+structure is added to an existing Jmol display using
+{\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} to open the Structure Chooser dialogue box.
+Select structures required and select {\sl View}. A new Jmol view
+opens containing superposed structures if the current selection contains two or more sequences with associated
structures.
\subsubsection{Obtaining the RMSD for a Superposition}
directly compared.
In order to recompute a superposition after changing a view or editing the
-alignment, select the {\sl Jmol $\Rightarrow$ Align sequences } menu option. The {\sl
-Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
+alignment, select the {\sl Jmol $\Rightarrow$ Align Structures} menu option.
+The {\sl Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
associated alignments and views are to be used to create the set of
correspondences. This menu is useful when composing complex superpositions
involving multi-domain and multi-chain complexes, when correspondences may be
prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
\end{list}
Jpred is launched in the same way as the other web services. Select {\sl Web
-Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
+Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
Secondary Structure Prediction}\footnote{JNet is the Neural Network based
secondary structure prediction method that the JPred server uses.} from the
alignment window menu (Figure \ref{jpred}).
Disordered regions in proteins were classically thought to correspond to
``linkers'' between distinct protein domains, but disorder can also play a role in
-function. The {\sl Web Services $\Rightarrow$ Disorder} menu in the alignment window
+function. The {\sl Web Service $\Rightarrow$ Disorder} menu in the alignment window
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
\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}
+clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$ 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
git://source.jalview.org / jalview-manual.git / commitdiff