X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=05bf2f15b006b73fd5fe196a20ef59403c71d6b4;hb=c350f93c6fac69b6a8a65645f0e89e26451df146;hp=c1c6ae79fe3c4f98b1d361570dbcc8269c4fd3c9;hpb=8d0464e6227795ef73b337205ce7f586976bb70c;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index c1c6ae7..05bf2f1 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,163 +1,175 @@ + -->
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: -
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.
+ + + ++ 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.