X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=3fa1563618d694bb5c60f86bef119893227fc465;hb=ccc31f21ed36c2e43b5a1b450846284151c680bb;hp=19f1761e97b0bfffce009cfde1a72e0a81a3e2ed;hpb=8d0464e6227795ef73b337205ce7f586976bb70c;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 19f1761..3fa1563 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,37 +1,45 @@ + -->
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
+
+ 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. +
+