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-
-
-
-The Chimera PDB Viewer
-
-
-
- The Chimera Viewer
-
-
- Since Jalview 2.8.2, Chimera
- (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
- structures opened via the "View
- Structure Data.." dialog.
-
-
- 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).
Please
- make sure your version of Chimera is up to date. Jalview requires
- at least Chimera version 1.11.1
-
-
- 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.
-
- Selecting residues in Jalview from Chimera
- When a selection is highlighted in a Jalview window, use the
- Select→Select Highlighted Region or press B
- to add the mapped positions to the alignment window's column
- selection.
Hint: Use your machine's 'switch
- application' key combination (Alt-Tab on Windows and Linux,
- Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview
- before pressing 'B' to select highlighted regions.
-
-
- 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.
-
-
- - Write Jalview
- features
Selecting this option will create
- new residue attributes for any features currently visible in
- the associated alignment views, allowing those positions to
- be selected and analysed with via Chimera's 'Render by
- Attribute' tool (found in the Tools submenu called Structure
- Analysis).
If you use this option, please
- remember to select the Refresh Menus option in
- Chimera's Render by Attribute dialog box in order to see the
- attributes derived from Jalview sequence features.
-
- - Fetch Chimera Attributes
This
- submenu lists available Chimera residue attributes that can
- be imported as Jalview features on associated sequences.
This
- is particularly useful for transferring quantitative
- positional annotation. For example, structure similarity for
- an alignment can be visualised by transferring the local
- RMSD attributes generated by Chimera's Match->Align tool
- onto aligned sequences and displayed with a Graduated feature colour
- scheme.
-
- - 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.
-
-