The Jmol PDB Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=ac2489ba9c2a90b0d59c01015275df83d4c13832;hb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;hp=e7f963b5ef213cf9c4ab6c911eb246fa28ab325e;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index e7f963b..ac2489b 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,167 +1,276 @@ - - - -The Jmol PDB Viewer - - -

The Jmol PDB Viewer -

The interactive structure viewing window is opened by selecting -the "Sequence→View PDB entry:" entry in -the sequence id pop-up menu. This -can only be done for sequences which have an associated -PDB structure. -

Since Jalview 2.3, Jmol -has been integrated into Jalview. It is automatically used by the -application, and should also run in the applet in all latest web -browsers. If jmol is not available, then the original internal pdb viewer will be used as a fallback. -

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 four 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. -
-
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 view, including any Uniprot sequence features or - region colourings.
  - 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.
- Standard and User Defined Jalview - colourschemes.
  - The remaining entries apply the colourschemes available from the - standard and user defined amino - acid colours.
-
Help
- Jmol Help
  Access the Jmol Help - documentation in a new browser window. -
-

Functionality provided by Jmol -

The Jmol menu 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.

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 documenation.

- - + + + +The Jmol PDB Viewer + + +

+ 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 shown + in a view, you can superimpose them using the corresponding + positions from the alignment via the Jmol→Align + menu option from the menu bar of the structure view window.
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: +

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. +

+ +

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