<strong>The Pymol Viewer</strong>
</p>
<p>
- In Jalview 2.11.2, support was added for <a href="https://pymol.org/2/">Pymol</a>
- (https://pymol.org/2/) to be used for viewing
- structures opened via the <a href="structurechooser.html"><strong>"View
- Structure Data.."</strong> dialog</a>.
+ In Jalview 2.11.2, support was added for viewing structures opened
+ via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a> with <a
+ href="https://pymol.org/2/">Pymol</a> (https://pymol.org/2/). Like
+ with <a href="chimera.html">Chimera and ChimeraX</a>, Pymol views
+ can be saved and restored from Jalview Project files on any machine
+ with it installed, and structures can be coloured and superimposed
+ according to the alignment.
</p>
<p>
- You can configure Pymol as your preferred structure viewer in
- <a href="preferences.html#structure"> Preferences</a>. You can also
- optionally specify the path to the Pymol program here (if it differs
- from the standard paths searched by Jalview).<br /> <strong>Jalview
- requires Pymol's RPC interface, which is not available in older
- versions of the Pymol community edition.<br />Please make sure your
- version of Pymol is up to date.
- </strong>
- </p>
+ <em>Configuring Jalview to use Pymol</em><br /> You can configure
+ Pymol as your preferred structure viewer in <a
+ href="preferences.html#structure"> Preferences</a>. Jalview will
+ look for an existing installation, and will ask you to specify the
+ installation's path if it cannot be found. You can also optionally
+ specify the path to the Pymol program here if you want Jalview to
+ use a specific installation.
+ </p>
+ <p>
+ <strong>Jalview requires Pymol V 2.5.0 (community edition)
+ or later</strong> <br />Jalview requires Pymol's RPC interface, which is
+ not available in older versions of the Pymol community edition.
+ </p>
<p>
- If you save your Jalview session as a project file, the state of any
- open Pymol windows will also be saved, and can be reopened by
- loading the project file on any machine with Pymol installed.
- </p>
- <p>
- <strong>Known Limitations</strong><br /> Jalview provides an easy way
- to employ Pymol for linked analysis of sequences and structures in the
- same way as <a href="chimera.html">Chimera and ChimeraX</a>. There are
- some limitations, however:
- </p>
- <ul>
- <li>Pymol does not support some forms of legacy structural data
- (e.g. the 1A70 C-alpha only PDB file included in the Jalview example
- project).</li>
- <li>Pymol to Jalview communication does not support transfer of
- properties or highlighting sequence regions corresponding to
- structure selections or mouse-overs in Pymol.</li>
- </ul>
+ <strong>Known Limitations</strong><br />
+ </p>
+ <ul>
+ <li>Pymol does not support some forms of legacy structural data
+ (e.g. the 1A70 C-alpha only PDB file included in the Jalview
+ example project).</li>
+ <li>Pymol to Jalview communication does not support transfer of
+ properties or highlighting sequence regions corresponding to
+ structure selections or mouse-overs in Pymol.</li>
+ <li>Jalview to Pymol communication currently doesn't highlight
+ the positions on structures corresponging to moused over residues
+ in Jalview.</li>
+ </ul>
<p>
Basic screen operations (see <a
- href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a> at
- https://pymol.org/dokuwiki/doku.php?id=mouse
- for full details).
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a>
+ at https://pymol.org/dokuwiki/doku.php?id=mouse for full details).
<table border="1">
<tr>
<td><strong>Action</strong></td>
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>Pymol<br>
- </strong><em>This pulldown menu provides access to Pymol's capabilities from Jalview.</em>
+ </strong><em>This pulldown menu provides access to Pymol's capabilities
+ from Jalview.</em>
<ul>
<li><strong><a name="sAlign">Align</a> <br> </strong><em>
When selected, the associated alignment will be used to
superimpose all the structures in the view onto the first
- structure in the alignment. The regions used to calculate
+ structure in the alignment via the pair_fit command. The regions used to calculate
the superposition will be highlighted using the 'Cartoon'
rendering style, and the remaining data shown as a chain
- trace.<br />
- <br />
+ trace. RMSD values are output in the Pymol log.<br /> <br />
</em></li>
<li><a name="annotxfer"><strong>Write Jalview
features</strong></a><br /> <em>Selecting this option will create
new atom properties for any features currently visible in
- the associated alignment views. This allows those atoms to
- be selected and analysed in Pymol directly.
- </em><br>
- <ul><li>Feature transfer in Pymol is experimental.</li><li>To select by a particular feature use the string matching syntax:<br>
- select foo,p.jv_helix in helix
- </li>
- <li>To view transferred properties use Pymol's Properties Inspector</li><li>
- For more information see <a href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property based selection in Pymol's Documentation</a>.
- </li>
- </ul>
- </li>
+ the associated alignment views. This allows those atoms to
+ be selected and analysed in Pymol directly. </em><br>
+ <ul>
+ <li>Feature transfer in Pymol is experimental.</li>
+ <li>To select by a particular feature use the string
+ matching syntax:<br> select foo,p.jv_helix in helix
+ </li>
+ <li>To view transferred properties use Pymol's
+ Properties Inspector</li>
+ <li>For more information see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property
+ based selection in Pymol's Documentation</a>.
+ </li>
+ </ul></li>
</ul></li>
<li><strong>Help<br>
</strong>
<ul>
<li><strong>Pymol Help<br>
- </strong><em>Access the Pymol Help documentation in a new browser window.
- window.</em></li>
+ </strong><em>Access the Pymol Help documentation in a new browser
+ window. window.</em></li>
</ul></li>
</ul>
<p>
<strong>Pymol and Windows Firewall</strong>
</p>
- Jalview and Pymol communicate using the <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
-
-<br> Technically this requires both Pymol and Jalview to open
+ Jalview and Pymol communicate using the
+ <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over
+ HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+
+ <br> Technically this requires both Pymol and Jalview to open
ports on the local network, and this may be blocked by Windows
Firewall with a warning message such as
<br /> "Windows Firewall has blocked some features of this program"
git://source.jalview.org / jalview.git / commitdiff