X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=e1227de7541038ed6ca28ee7d2df0a4eb5ee4c57;hb=1f3cf1db69c97ace5c0606e2ee0ccbf569970761;hp=5ae00afe9955a5e36d1f89b0e1db7a8e8c02d6ea;hpb=a818865e1c7ea11c5a02d5bd90d4860125aa0350;p=jalview.git
diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 5ae00af..e1227de 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -211,8 +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.
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