The Jmol PDB Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=c6508f937a1728fd82d05db59bca35bc49f9360c;hb=c42bc457ef9b3a5606f309268d4a644ef113c390;hp=66edaf9c3e5243d224a5ac331ba517768e2ebf4e;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 66edaf9..c6508f9 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,6 +1,6 @@ + +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.

+ +

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