The Jmol PDB Viewer -
The interactive structure viewing window is opened by selecting -the "Sequence→View PDB entry:" entry in -the sequence id pop-up menu. This -can only be done for sequences which have an associated -PDB structure. +
The Jmol PDB Viewer
Since Jalview 2.3, Jmol -has been integrated into Jalview. It is automatically used by the -application, and should also run in the applet in all latest web -browsers. If jmol is not available, then the original internal pdb viewer will be used as a fallback. +has been integrated into Jalview for interactively viewing structures +opened by selecting the "Sequence→View PDB +entry:" option in the sequence +id pop-up menu (if you can't see this, then you need to associate a PDB structure with the +sequence). Jmol is available from the Jalview desktop and should also +run in the JalviewLite applet, providing the browser supports Java 1.5. +If Jmol is not available, then the original internal +pdb viewer will be used as a fallback.
+Superposing structures based
+on their aligned sequences
+If several structures are available on the alignment, you may add
+additional structures to an existing Jmol view by selecting their entry
+in the appropriate pop-up menu. Jalview will ask you if you wish to add
+the structure to the existing alignment, and if you do, it will import
+and superimpose the new PDB file using the corresponding positions from
+the alignment. If the alignment is subsequently edited, you can use the
+Jmol→Align menu option from the
+menu bar of the structure view window to superpose the structures using
+the updated alignment.
+Sequence based structure superposition was added in Jalview 2.6
Controls
-The structure is by default rendered as a ribbon diagram. Moving the -mouse over the structure brings up tooltips giving the residue name, -PDB residue number and chain code, atom name and number +
Controls
+The structure is by default rendered as a ribbon diagram. Moving the
+mouse over the structure brings up tooltips giving the residue name, PDB
+residue number and chain code, atom name and number
([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue
-in any associated sequences, then this will be highlighted in each
-one's alignment window. The converse also occurs - moving the mouse
-over an associated residue in an alignment window highlights the associated
+in any associated sequences, then this will be highlighted in each one's
+alignment window. The converse also occurs - moving the mouse over an
+associated residue in an alignment window highlights the associated
atoms in the displayed structures.
Selecting a residue highlights its associated sequence residue and alpha carbon location. Double clicking an atom allows distances to @@ -60,9 +72,11 @@ be measured from it to any other atom in the structure.
The window has four menus: +
The window has up to five menus:
Functionality provided by Jmol -
The Jmol menu provides access to a number of features for +
Functionality provided by Jmol
+Jmol's own functions are accessed by clicking the 'Jmol' logo or +right-clicking in the structure display area. Either way will open the +Jmol pop-up menu, which provides access to a number of features for controlling the colour and display of molecules, adding measurements and -labels, plotting surfaces, and display animation. The 'Set Picking' -menu controls the behaviour of single and double mouse clicking on the -structure.
+labels, plotting surfaces, and display animation. The 'Set Picking' menu +controls the behaviour of single and double mouse clicking on the +structure, and the 'Console' option opens the Jmol scripting console.The state of each Jmol display is stored within jalview archives as a jmol state recovery script -file. This means that any Jmol visualization effects that -you add beyond those provided by Jalview will be able to be stored and -recovered along with the displayed alignments in Jalview. -
More Information -
Jmol is a sophisticated program in its own right, with its own + href="jalarchive.html">jalview archives as a Jmol state recovery +script file. This means that any Jmol visualization effects that you add +beyond those provided by Jalview will be able to be stored and recovered +along with the displayed alignments in Jalview.
+More Information
+Jmol is a sophisticated program in its own right, with its own command console and scripting language. Only the essentials have been -described here - the interested reader is referred to -Jmol's own comprehensive -online documenation.
+described here - the interested reader is referred to Jmol's own comprehensive +online documentation. +