X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=5ae00afe9955a5e36d1f89b0e1db7a8e8c02d6ea;hb=0935f3c68446aa5cd3a928295a0c5ea78f303648;hp=e80d0e2ad7a9aaff65f475a9767cc46f57229fe8;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git
diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index e80d0e2..5ae00af 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -1,7 +1,7 @@
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).
@@ -181,7 +171,7 @@
Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment views, including any
- Uniprot sequence features or region colourings.
Pick
+ UniProt sequence features or region colourings.
Pick
which of the associated alignment views are used to colour
the structures using the View→Colour
by .. sub menu.
@@ -205,8 +195,8 @@
colourschemes.
The remaining entries apply the colourschemes available
from the standard and user defined amino acid colours.
+ href="../colourSchemes/index.html">amino acid
+ colours.
Chimera
@@ -237,8 +227,8 @@
Jalview and Chimera communicate using Chimera's
REST service
+ href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST
+ service
(http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
Technically this requires both Chimera and Jalview to open
ports on the local network, and this may be blocked by Windows