<ul>
<li>Standard installation on Linux/Unix:<pre>
- /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
</li>
<li>Standard installation on Windows:<pre>
\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
</p>
<p>
<strong>Passing JVM Arguments to Jalview</strong><br /> If you need
- to modify parameters for Jalview's Java Virtual Machine, then take a
- look at the instructions for how to <a href="../memory.html#jvm">setting
- the JVM's maximum memory</a>.
+ to modify parameters for Jalview's Java Virtual Machine, or
+ configure system properties, then take a look at the instructions
+ for how to <a href="../memory.html#jvm">setting the JVM's
+ maximum memory</a>.<br />
+ <p>
+ <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
+ are experiencing issues with the font size or layout of Jalview's
+ GUI, you can try changing Jalview's 'Look and feel' by
+ specifying a custom system property 'laf' on startup (see <a
+ href="../memory.html#jvm">setting the JVM's memory</a> for
+ instructions on how to do this for your platform). <br />For the
+ Jalview standalone executable jar, simply provide one of the
+ property settings before the -jar argument
</p>
+ <ul>
+ <li>-Dlaf=system (default look and feel for the OS)</li>
+ <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
+ <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
+ <li>-Dlaf=mac (only has an effect on OSX)</li>
+ <li>-Dlaf=gtk (only has an effect on Linux)</li>
+ </ul>
+ The currently configured look and feel is logged to Jalview's console.
+ Once the look and feel has been changed, it will be stored in
+ Jalview's .jalview_properties file for future Jalview sessions.
+
<p> </p>
<p> </p>
</body>