X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=ce1b8341d7e464628323edd8117bc16f37d20b74;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=e7f963b5ef213cf9c4ab6c911eb246fa28ab325e;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index e7f963b..ce1b834 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,167 +1,236 @@ - - -
-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.
- - + + + +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.
+ + +