X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=05bf2f15b006b73fd5fe196a20ef59403c71d6b4;hb=806c9dc4a3d841fe36e7d17ab45d783a9fc95f26;hp=b29d2ae622289f30e5b5a76a02c9335bfaae7976;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
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 -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, 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.