X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=e1227de7541038ed6ca28ee7d2df0a4eb5ee4c57;hb=0bee8aadc22e41e4793db251a7d37a839bd77db8;hp=485466af73b238f939340acf6e32885e392d78e3;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git
diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 485466a..e1227de 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
@@ -221,8 +211,30 @@
structure in the alignment. The regions used to calculate
the superposition will be highlighted using the 'Cartoon'
rendering style, and the remaining data shown as a chain
- trace.
+ trace.
+
+
+ Write Jalview
+ features
Selecting this option will create
+ new residue attributes for any features currently visible in
+ the associated alignment views, allowing those positions to
+ be selected and analysed with via Chimera's 'Render by
+ Attribute' tool (found in the Tools submenu called Structure
+ Analysis).
If you use this option, please
+ remember to select the Refresh Menus option in
+ Chimera's Render by Attribute dialog box in order to see the
+ attributes derived from Jalview sequence features.
+ Fetch Chimera Attributes
This
+ submenu lists available Chimera residue attributes that can
+ be imported as Jalview features on associated sequences.
This
+ is particularly useful for transferring quantitative
+ positional annotation. For example, structure similarity for
+ an alignment can be visualised by transferring the local
+ RMSD attributes generated by Chimera's Match->Align tool
+ onto aligned sequences and displayed with a Graduated feature colour
+ scheme.
Help
@@ -237,8 +249,8 @@
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