X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=3fa1563618d694bb5c60f86bef119893227fc465;hb=d8b9b83f2739ee2c11670af890d2c63b8c1c2b7c;hp=5102679dbba9e4aece5ddeda7d2c2ab07223846e;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git
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+
+ 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:
+
+ - File
+
+
+ - Save As
+ Save the displayed PDB File, or the current view as an
+ EPS or PNG file.
+ - View Mapping
+ Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.
+
+ - View
+
+ - Show Chains
+ Select which of the PDB file's chains are to be
+ displayed.
+ - Colour by ..
Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:
+
+ - Select many views
When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.
+ - Select all views
This
+ is only enabled when Select many views
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.
+ - Invert selection
This
+ is only enabled when Select many views
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.
+
+
+ - Colours
+
+
+ - By Sequence
+ Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ Uniprot sequence features or region colourings.
Pick
+ which of the associated alignment views are used to colour
+ the structures using the View→Colour
+ by .. sub menu.
+
Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.
+ - By Chain
+ Assigns a random colour to each PDB chain.
+ - Charge & Cysteine
+ Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.
+ - Colour with Jmol
Defers
+ any colouring operations to Jmol. Select this if you want to
+ use the Jmol scripting interface or menu to modify the view
+ directly.
+ - Standard and User Defined Jalview
+ colourschemes.
+ The remaining entries apply the colourschemes available
+ from the standard and user defined amino acid colours.
+
+
+ - Jmol
+ This pulldown menu is only displayed if there are multiple
+ structures shown in the Jmol window, and Jalview can also locate
+ at least two of the structures in the currently associated
+ alignment view.
+
+ - Align
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace.
(This option was introduced in Jalview 2.6)
+
+
+ - Help
+
+
+ - Jmol Help
+ Access the Jmol Help documentation in a new browser
+ window.
+
+
+
+
+ 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.
+
+