X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=0cd6168475804038b778b44eb3e0c7a094bc131e;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=e7f963b5ef213cf9c4ab6c911eb246fa28ab325e;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index e7f963b..0cd6168 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,167 +1,282 @@ - - -
-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. +
+ +
+ 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. Press B or use
+ Select→Select Highlighted columns from any linked
+ alignment window to mark the columns highlighted after mousing over
+ the structure.
+
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. +
+ + +