X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=21241d3ee5f27d392a6e0319e914f9606e80fe3f;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=66edaf9c3e5243d224a5ac331ba517768e2ebf4e;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 66edaf9..21241d3 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,18 +1,234 @@ - - + + +
+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.
+The following menu entries are provided for viewing structure data
+
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.
+ + +