X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=2bfaeb652cce9d93cd6982e2292b651984e90baf;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=a7e2c108442a85413d4919c35eaf33ed754f1d0d;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index a7e2c10..2bfaeb6 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,45 +1,165 @@ - -
Viewing PDB Structures
-Jalview has a simple 3D structure viewer which can load PDB files and associate - the structure with a sequence in an alignment.
-There are 2 ways to load and associate a PDB file into Jalview application.
-Note 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.
-To see a particular structure, right click on a sequence name and from the - popup menu select "Sequence -> View PDB Entry".
-The PDB Structure viewer will perform a pairwise alignment of your sequence - and each PDB chain sequence. To view the results of the mapping, select "File - -> View Mapping" from the structure viewer window.
-Moving the mouse over the structure will highlight the residue in the alignment - window, and vice versa.
-"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate - residues red, Lysine and Arginine will be blue and Cysteine residues will be - coloured yellow.
-Tips for Viewing Structures
-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.
+ +