X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=0cd6168475804038b778b44eb3e0c7a094bc131e;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=8a5d75b1635d6bb8870eb0bf2b3db4baf1ccebdc;hpb=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 8a5d75b..0cd6168 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,214 +1,282 @@ - - -
-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. +
+ +
+ 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. +
+ + +