Superposing structures based on
- their aligned sequences
If several structures are
- available on the alignment, you may add additional structures to an
- existing Jmol view by selecting their entry in the appropriate
- pop-up menu. Jalview will ask you if you wish to add the structure
- to the existing alignment, and if you do, it will import and
- superimpose the new PDB file using the corresponding positions from
- the alignment. If the alignment is subsequently edited, you can use
- the Jmol→Align menu option from
- the menu bar of the structure view window to superpose the
- structures using the updated alignment.
Sequence
+ their aligned sequences
If several structures are shown
+ in a view, you can superimpose them using the corresponding
+ positions from the alignment via the Jmol→Align
+ menu option from the menu bar of the structure view window.
Sequence
based structure superposition was added in Jalview 2.6
- Controls
The structure is by default
- rendered as a ribbon diagram. Moving the mouse over the structure
- brings up tooltips giving the residue name, PDB residue number and
- chain code, atom name and number
- ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a
- residue in any associated sequences, then this will be highlighted
- in each one's alignment window. The converse also occurs - moving
- the mouse over an associated residue in an alignment window
- highlights the associated atoms in the displayed structures.
+ Controls
The structure is by default rendered
+ as a ribbon diagram. Moving the mouse over the structure brings up
+ tooltips giving the residue name, PDB residue number and chain code,
+ atom name and number ([RES]Num:Chain.AtomName#AtomNumber). If a
+ mapping exists to a residue in any associated sequences, then this
+ will be highlighted in each one's alignment window. The converse
+ also occurs - moving the mouse over an associated residue in an
+ alignment window highlights the associated atoms in the displayed
+ structures. Press B or use
+ Select→Select Highlighted columns from any linked
+ alignment window to mark the columns highlighted after mousing over
+ the structure.
Selecting a residue highlights its associated sequence residue
and alpha carbon location. Double clicking an atom allows distances
@@ -195,7 +192,7 @@
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.
@@ -218,8 +215,8 @@
colourschemes.
The remaining entries apply the colourschemes available
from the standard and user defined amino acid colours.
+ href="../colourSchemes/index.html">amino acid
+ colours.
@@ -259,11 +256,10 @@
Jmol scripting console.
The state of each Jmol display is stored within Jalview archives as a Jmol state recovery script file. This means - that any Jmol visualization effects that you add beyond those - provided by Jalview will be able to be stored and recovered along - with the displayed alignments in Jalview. + href="jalarchive.html">Jalview archives as a Jmol state + recovery script file. This means that any Jmol visualization effects + that you add beyond those provided by Jalview will be able to be + stored and recovered along with the displayed alignments in Jalview.
More Information @@ -272,8 +268,8 @@ Jmol is a sophisticated program in its own right, with its own command console and scripting language. Only the essentials have been described here - the interested reader is referred to Jmol's own comprehensive online documentation. + href="http://jmol.sourceforge.net/docs/">Jmol's own + comprehensive online documentation.