X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=21241d3ee5f27d392a6e0319e914f9606e80fe3f;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=a10b14e8df83f63780cf5148c117c494f455a673;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index a10b14e..21241d3 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,214 +1,234 @@ - - -
-The Jmol PDB Viewer
-Since Jalview 2.3, Jmol -has been integrated into Jalview for interactively viewing structures -opened by selecting the "Structure→View PDB -entry:" option 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.
- - - + + + +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.
+ + +