X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=05bf2f15b006b73fd5fe196a20ef59403c71d6b4;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=a7e2c108442a85413d4919c35eaf33ed754f1d0d;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index a7e2c10..05bf2f1 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,45 +1,175 @@ - -
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.
+ +