The Chimera PDB Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=68ac4652fbb80e0ba7aeb611ec0ec42e0161a224;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=31ca419adb802db7b7383f45db2968c45e424023;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 31ca419..68ac465 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -23,153 +23,253 @@ 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/) 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:

The "Structure→View - Structure→ submenu allows a single PDB structure to be chosen - for display from the available structures for a sequence. -
The "Structure→View all N - structures - option will open a new window containing all structures associated - with the current selection. -
The "Structure→View all N - representative structures - option will open a new window containing exactly one structure per - currently selected sequence.
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.

+
EXPERIMENTAL FEATURES
+ + These are only available if the Tools→Enable + Experimental Features option is enabled. (Since Jalview 2.10.2) +
- 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. +
  + View + this function's issue in Jalview's bug tracker
- 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. + View + this function's issue in Jalview's bug tracker
Help
+ +
- Chimera Help
  + Access the Chimera Help documentation in a new browser + window.

-
-

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. For comprehensive details of Chimera's commands, refer to the tool's Help menu.

Basic screen operations (see Chimera help -(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
-

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.

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)