X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=68ac4652fbb80e0ba7aeb611ec0ec42e0161a224;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=1b0b9c192d5a51852af8057ee558b9e844c9b5af;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 1b0b9c1..68ac465 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
@@ -201,10 +211,41 @@
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.
-
-
+
+
+ These are only available if the Tools→Enable
+ Experimental Features option is enabled. (Since Jalview 2.10.2)
+
+
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.
+
+ View
+ this function's issue in Jalview's bug tracker
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.
+ View
+ this function's issue in Jalview's bug tracker