X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=e1227de7541038ed6ca28ee7d2df0a4eb5ee4c57;hb=4e60a6952c6b85e10335b3feb5fef6c81bba79a4;hp=1b0b9c192d5a51852af8057ee558b9e844c9b5af;hpb=dde303bc73617ab4eb3e681e67cf899e6a971318;p=jalview.git diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 1b0b9c1..e1227de 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -65,9 +65,19 @@ 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
@@ -201,8 +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.
+
+
+
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.
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.