<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
structures opened by entries in the <strong>"Structure"</strong>
submenu in the <a href="../menus/popupMenu.html">sequence id
pop-up menu</a> (if you can't see this, then you need to <a
- href="viewingpdbs.html"
- >associate a PDB structure</a> with the sequence). Jmol is available
- from the Jalview desktop and should also run in the JalviewLite
- applet, providing the browser supports Java 1.5. If Jmol is not
- available, then the original <a href="pdbviewer.html">internal
- pdb viewer</a> will be used as a fallback.
+ href="viewingpdbs.html">associate a PDB structure</a> with
+ the sequence). Jmol is available from the Jalview desktop and should
+ also run in the JalviewLite applet, providing the browser supports
+ Java 1.5. If Jmol is not available, then the original <a
+ href="pdbviewer.html">internal pdb viewer</a> will be used as a
+ fallback.
</p>
<!-- <p>The following menu entries are provided for viewing structure data<br>
<ul>
</p> -->
<p>
<a name="align"><strong>Superposing structures based on
- their aligned sequences</strong></a><br> 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 <a href="#sAlign"><em>Jmol→Align</em></a> menu option from
- the menu bar of the structure view window to superpose the
- structures using the updated alignment.<br> <em>Sequence
+ their aligned sequences</strong></a><br> If several structures are shown
+ in a view, you can superimpose them using the corresponding
+ positions from the alignment via the <a href="#sAlign"><em>Jmol→Align</em></a>
+ menu option from the menu bar of the structure view window. <br> <em>Sequence
based structure superposition was added in Jalview 2.6</em>
</p>
<p>
- <strong>Controls</strong><br> 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.
+ <strong>Controls</strong><br> 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
+ <em>Select→Select Highlighted columns</em> from any linked
+ alignment window to mark the columns highlighted after mousing over
+ the structure.
</p>
<p>Selecting a residue highlights its associated sequence residue
and alpha carbon location. Double clicking an atom allows distances
</strong><em> 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.<br />Pick
+ UniProt sequence features or region colourings.<br />Pick
which of the associated alignment views are used to colour
the structures using the <strong>View→Colour
by ..</strong> sub menu.
colourschemes.<br>
</strong><em>The remaining entries apply the colourschemes available
from the standard and user defined <a
- href="../colourSchemes/index.html"
- >amino acid colours</a>.
+ href="../colourSchemes/index.html">amino acid
+ colours</a>.
</em></li>
</ul></li>
<li><strong>Jmol<br>
Jmol scripting console.</p>
<p>
The state of each Jmol display is stored within <a
- href="jalarchive.html"
- >Jalview archives</a> 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</a> 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.
</p>
<p>
<strong>More Information</strong>
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 <a
- href="http://jmol.sourceforge.net/docs/"
- >Jmol's own comprehensive online documentation</a>.
+ href="http://jmol.sourceforge.net/docs/">Jmol's own
+ comprehensive online documentation</a>.
</p>
</p>
</body>
git://source.jalview.org / jalview.git / blobdiff