X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=39dff7534e127825a20236e777e77df07c4e79bc;hb=409fd993c6e32e999b24082aae107a043a590f8f;hp=31ca419adb802db7b7383f45db2968c45e424023;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
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--- a/help/html/features/chimera.html
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@@ -23,16 +23,31 @@
The Chimera PDB Viewer
-The Chimera Viewer
-Since Jalview 2.8.2, Chimera (http://www.cgl.ucsf.edu/chimera/)
-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). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.
-You can set a default choice of Jmol or Chimera structure viewer in Preferences.
-You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).
-
The following menu entries are provided for viewing structure data
+
+ The Chimera Viewer
+
+
+ Since Jalview 2.8.2, Chimera
+ (http://www.cgl.ucsf.edu/chimera/) 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). Chimera is
+ available from the Jalview desktop, provided Chimera has been
+ separately installed.
+
+
+ You can set a default choice of Jmol or Chimera structure viewer in
+ Preferences. You can also
+ optionally specify the path to the Chimera program here (if it
+ differs from the standard paths searched by Jalview).
+
+ If you save your Jalview session as a project file, the state of any
+ open Chimera windows will also be saved, and can be reopened by
+ loading the project file on any machine with Chimera installed. Since
+ Jalview 2.9.
+
+
+ Superposing structures based on
+ their aligned sequences
If several structures are
+ available on the alignment, you may add additional structures to an
+ existing Chimera 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 Chimera→Align menu option
+ from the menu bar of the structure view window to superpose the
+ structures using the updated alignment.
+
+
+ Chimera 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 ([RES]Num:Chain). Moving the mouse over an
+ associated residue in an alignment window highlights the associated
+ atoms in the displayed structures. When residues are selected in the
+ Chimera window, they are highlighted on the alignment. For
+ comprehensive details of Chimera's commands, refer to the tool's
+ Help menu.
+
+ Basic screen operations (see Chimera help at
+ http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
+ for full details).
+
+
+ | Action |
+ Windows |
+ Unix |
+ Mac/OSX |
+
+
+ | Rotate View |
+ Left Click and Drag |
+ Left Click and Drag |
+ Left Click and Drag |
+
+
+ | Zoom |
+ Right Click
drag mouse up or down
+ |
+ Right Click
drag mouse up or down
+ |
+ cmd or Right + Click and drag mouse up or down,
or
+ use mouse scroll button
+ |
+
+
+ | Move Origin |
+ Middle Button + Drag |
+ Middle Button and drag |
+ alt + Click
and drag
+ |
+
+
+ | Select Residues |
+ Ctrl + Click (and drag to select a region) |
+ Ctrl + Click (and drag) |
+ Ctrl + Click (and drag) |
+
+
+
+
+ Jalview Controls
+
The Jalview Chimera View window has up to five menus:
+
+ - 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 (if more than
+ one) 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
+ Uses the Chimera 'rainbow chain' command to apply a
+ different colour to each 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 Chimera
Defers
+ any colouring operations to Chimera. Select this if you want
+ to use the Chimera 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.
+
+
+ - Chimera
+ This pulldown menu is only displayed if there are multiple
+ structures shown in the Chimera 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.
+
+
+ - Help
+
+
+ - Chimera Help
+ Access the Chimera Help documentation in a new browser
+ window.
+
+
+
+ Chimera and Windows Firewall
+
+ Jalview and Chimera communicate using Chimera's
+ REST service
+ (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
+
Technically this requires both Chimera and Jalview to open
+ ports on the local network, and this may be blocked by Windows
+ Firewall with a warning message such as
+
"Windows Firewall has blocked some features of this program"
+ (where the program may be jp2launcher.exe for Jalview Webstart, or
+ java.exe or javaw.exe for the InstallAnywhere version).
+
To allow Jalview and Chimera to interact, you may need to add
+ permission for the program to communicate over the network. This can
+ be done from the warning dialogue, or in Control Panel, Firewall
+ settings.