X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fchimera.html;h=68ac4652fbb80e0ba7aeb611ec0ec42e0161a224;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=e80d0e2ad7a9aaff65f475a9767cc46f57229fe8;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index e80d0e2..68ac465 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
    @@ -221,10 +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.

    • - -
  • Help
    +
  • EXPERIMENTAL FEATURES
    + + These are only available if the Tools→Enable + Experimental Features option is enabled. (Since Jalview 2.10.2) +
      +
    • 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. +
      + View + this function's issue in Jalview's bug tracker
      • +
    • 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. +       View + this function's issue in Jalview's bug tracker
      • +
    • +
  • Help
    • Chimera Help
      @@ -237,8 +258,8 @@

      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