X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=5ae00afe9955a5e36d1f89b0e1db7a8e8c02d6ea;hb=b6000a31609b8d7f6b9cca8df5d4878d393e2b24;hp=39dff7534e127825a20236e777e77df07c4e79bc;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 39dff75..5ae00af 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -28,43 +28,23 @@
Since Jalview 2.8.2, Chimera - (http://www.cgl.ucsf.edu/chimera/) has been integrated into Jalview - for interactively viewing structures 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). Chimera is - available from the Jalview desktop, provided Chimera has been - separately installed. + (http://www.cgl.ucsf.edu/chimera/) can be used for viewing + structures opened via the "View + Structure Data.." dialog.
You can set a default choice of Jmol or Chimera structure viewer in
Preferences. You can also
optionally specify the path to the Chimera program here (if it
- differs from the standard paths searched by Jalview).
+ differs from the standard paths searched by Jalview).
Please
+ make sure your version of Chimera is up to date. Jalview requires
+ at least Chimera version 1.11.1
+
If you save your Jalview session as a project file, the state of any open Chimera windows will also be saved, and can be reopened by loading the project file on any machine with Chimera installed. Since Jalview 2.9. -
Superposing structures based on
their aligned sequences
If several structures are
@@ -85,13 +65,23 @@
number and chain code ([RES]Num:Chain). Moving the mouse over an
associated residue in an alignment window highlights the associated
atoms in the displayed structures. When residues are selected in the
- Chimera window, they are highlighted on the alignment. For
- comprehensive details of Chimera's commands, refer to the tool's
- Help menu.
+ Chimera window, they are highlighted on the alignment.
+
For comprehensive details of Chimera's commands, refer to the + tool's Help menu.
+
+ Selecting residues in Jalview from Chimera
+ When a selection is highlighted in a Jalview window, use the
+ Select→Select Highlighted Region or press B
+ to add the mapped positions to the alignment window's column
+ selection.
Hint: Use your machine's 'switch
+ application' key combination (Alt-Tab on Windows and Linux,
+ Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview
+ before pressing 'B' to select highlighted regions.
+
Basic screen operations (see Chimera help at + href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera + help at http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html for full details).