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.
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.
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 four menus:
Functionality provided by Jmol
The Jmol menu 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.
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 documenation.