PDB Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=fd13f572162a6483f417d6640cf97714c1a53ed5;hb=c17661b22323a66090ea91e04751aa17461b17c5;hp=97471a2e9899777db4c7c60ab162e9cf3d2dab82;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index 97471a2..fd13f57 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,136 +1,176 @@ + PDB Viewer -

The PDB Viewer Window -

This 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.

Controls

The structure is rendered as an alpha-carbon trace. Moving the -mouse over the structure brings up tooltips with a residue name and PDB -sequence position. If a mapping exists to a residue in the associated -sequence, then this will be highlighted in the associated view in its -alignment window, and vice versa for viewing the coordinates associated -with a particular residue in the sequence in a particular view on the -alignment.

Selecting a residue highlights its associated sequence residue -and alpha carbon location.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Action Windows Unix Mac/OSX
Select/
- Deselect
- Residue Left Click Left Click Click
Rotate View Left Click and Drag Left Click and Drag Click and Drag
Roll View Right Click and drag Right Click and Drag TODO
Move Origin Middle-Button and Drag Middle-Button and Drag TODO
Zoom In Up Arrow Up Arrow Up Arrow
Zoom Out Down Arrow Down Arrow Down Arrow
-

There are three menus: -

File
- -
- Save As
  - Saves 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.
-
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.
-

View
- These options can be turned off to improve performance when - viewing large structures, some at the expense of visual clarity. -

Wireframe
- Draws thin lines rather than thick lines for the - alpha-carbon trace.
Depthcue
- Shades the structure so parts of the structure near the front - of the view are brighter than those further away.
Z Buffering
- Applies depth sorting to correctly render occluded regions - of the backbone trace.
Show All Chains
- When turned on, shows all chains in the PDB file, not just - the one associated with a sequence in the alignment window.

Associate View
+

+ The Jalview internal PDB Viewer
Since + Jalview 2.3, the Jmol PDB Viewer is the main + method for viewing PDB structures. + The documentation below concerns the original Jalview PDB viewer, + which is only used in situations where Jmol is unavailable or cannot + operate. +

+ The PDB Viewer Window +

+ This interactive structure viewing window is opened by selecting + entries from the "Structure→" + submenu of the sequence id + pop-up menu. The internal PDB viewer is not able to show + superpositions, so no other options are provided. Structures can + only be viewed for sequences which have an associated PDB structure, and the PDB Viewer will only be + associated with the particular alignment view from which it was + opened. +

+ Controls +

The structure is rendered as an alpha-carbon trace. Moving the + mouse over the structure brings up tooltips with a residue name and + PDB sequence position. If a mapping exists to a residue in the + associated sequence, then this will be highlighted in the associated + view in its alignment window, and vice versa for viewing the + coordinates associated with a particular residue in the sequence in + a particular view on the alignment.

Selecting a residue highlights its associated sequence residue + and alpha carbon location.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Action Windows Unix Mac/OSX
Select/
Deselect
Residue + Left Click Left Click Click
Rotate View Left Click and Drag Left Click and Drag Click and Drag
Roll View Right Click and drag Right Click and Drag TODO
Move Origin Middle-Button and Drag Middle-Button and Drag TODO
Zoom In Up Arrow Up Arrow Up Arrow
Zoom Out Down Arrow Down Arrow Down Arrow
+

There are three menus: +

File
+ +
- Save As
  + Saves 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.
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.
View
+ These options can be turned off to improve performance + when viewing large structures, some at the expense of visual + clarity. +
- Wireframe
  + Draws thin lines rather than thick lines for the + alpha-carbon trace.
- Depthcue
  + Shades the structure so parts of the structure near the + front of the view are brighter than those further away.
- Z Buffering
  + Applies depth sorting to correctly render occluded + regions of the backbone trace.
- Show All Chains
  + When turned on, shows all chains in the PDB file, not + just the one associated with a sequence in the alignment + window.

+ Notes for PDB Viewing in the Jalview Applet +

The applet can only load PDB files by copying and pasting the + text into the popup window which appears when "Show PDB + Structure" is selected after right clicking on a sequence name.

Action	Windows	Unix	Mac/OSX
Select/ - Deselect - Residue	Left Click	Left Click	Click
Rotate View	Left Click and Drag	Left Click and Drag	Click and Drag
Roll View	Right Click and drag	Right Click and Drag	TODO
Move Origin	Middle-Button and Drag	Middle-Button and Drag	TODO
Zoom In	Up Arrow	Up Arrow	Up Arrow
Zoom Out	Down Arrow	Down Arrow	Down Arrow