X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fjmol.html;h=c81fcc39fdb4550f8e4aa07438c64034b46e03db;hb=b1cc8e6f8f1a20e6934b87305ceda18f828fdfd2;hp=b3c35704691486c065b89aa41c193be6aa21606c;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index b3c3570..c81fcc3 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -1,22 +1,24 @@ + --> The Jmol PDB Viewer @@ -24,14 +26,33 @@

The Jmol PDB Viewer

Since Jalview 2.3, Jmol has been integrated into Jalview for interactively viewing structures -opened by selecting the "Structure→View PDB -entry:" option in the sequence +opened by entries in the "Structure" submenu in the sequence id pop-up menu (if you can't see this, then you need to associate a PDB structure with the sequence). Jmol is available from the Jalview desktop and should also run in the JalviewLite applet, providing the browser supports Java 1.5. If Jmol is not available, then the original internal pdb viewer will be used as a fallback.

+

Superposing structures based on their aligned sequences
If several structures are available on the alignment, you may add @@ -58,7 +79,7 @@ atoms in the displayed structures.

and alpha carbon location. Double clicking an atom allows distances to be measured from it to any other atom in the structure.

- +
@@ -141,7 +162,7 @@ be measured from it to any other atom in the structure.

  • Select all views
    This is only enabled when Select many views is also enabled, and will add all associated views to the set used to colour the structure display.
  • Invert selection
    This is only enabled when Select many views is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display. -
    • +
  • Colours
    • Action Windows