X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=05bf2f15b006b73fd5fe196a20ef59403c71d6b4;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index e18e273..05bf2f1 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,18 +1,175 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +PDB Viewer + + +

+ 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.

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ActionWindowsUnixMac/OSX
Select/
Deselect
Residue +
Left ClickLeft ClickClick
Rotate ViewLeft Click and DragLeft Click and DragClick and Drag
Roll ViewRight Click and dragRight Click and DragTODO
Move OriginMiddle-Button and DragMiddle-Button and DragTODO
Zoom InUp ArrowUp ArrowUp Arrow
Zoom OutDown ArrowDown ArrowDown 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.

+ +