The Jmol PDB Viewer
Since Jalview 2.3, Jmol has been integrated into Jalview for interactively viewing structures opened by entries in the "Structure" submenu 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
([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
atoms in the displayed structures.
Selecting a residue highlights its associated sequence residue and alpha carbon location. Double clicking an atom allows distances to be measured from it to any other atom in the structure.
Action | Windows | Unix | Mac/OSX |
Rotate View | Left Click and Drag | Left Click and Drag | Click and Drag |
Zoom | Shift + Left Click drag mouse up or down |
Shift + Left Click or middle button drag mouse up or down |
Left-Alt + Click and drag mouse up or down |
Select/ Deselect Residue |
Left Click | Left Click | Click |
Roll View | Shift + Left Click drag mouse to left or right |
Shift + Left Click or middle button drag mouse to left or right |
Left-Alt + Click and drag mouse to left or right |
Move Origin | Shift+Control+Left Click or Middle Button + Drag |
Middle-Button and drag |
Shift+Control+Left Click or Middle Button and drag |
Jmol Menu | Right-Click | Right-Click | Apple-Click |
The window has up to five menus:
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, 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 command console and scripting language. Only the essentials have been described here - the interested reader is referred to Jmol's own comprehensive online documentation.