X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=05bf2f15b006b73fd5fe196a20ef59403c71d6b4;hb=c350f93c6fac69b6a8a65645f0e89e26451df146;hp=97471a2e9899777db4c7c60ab162e9cf3d2dab82;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index 97471a2..05bf2f1 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,136 +1,175 @@ +
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: -
+ 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.