X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=2bfaeb652cce9d93cd6982e2292b651984e90baf;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=bd240ea4bd2b9d4ea492dfdfd309c40296771af2;hpb=f850089f8bc67403194f4a1a3b793a46dbb4224a;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index bd240ea..2bfaeb6 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,93 +1,165 @@ - -
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 alignment window, and vice versa for viewing the coordinates -associated with a particular residue in the sequence.
-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.
- - + + + +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.
+ +