The Jmol PDB Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=2f1019660d74b8127338e8b6beba1dc16fc676c6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=9d0ad11ad536b1ef7cf5f6c1047dc76facadf6ce;hpb=0943de76f6a7435894e72479671642c05f2f3687;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 9d0ad11..2f10196 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -23,17 +23,23 @@ 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 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.

+ 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. +

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