</li>
<li>The <a href="#connections"><strong>"Connections"</strong>
Preferences</a> tab allows you to configure Jalview's internet
- settings and specify your default web browser.
+ settings.
</li>
<li>The <a href="#links"><strong>"Links"</strong>
Preferences</a> tab shows the currently configured <em>URL
<li>The <a href="#editing"><strong>"Editing"</strong>
Preferences</a> tab contains settings affecting behaviour when editing alignments.
</li>
+ <li>The <a href="#startup"><strong>"Startup"</strong>
+ Preferences</a> tab allows you to adjust how much memory is
+ allocated to Jalview when it is launched.
+ </li>
<li>The <a href="#hmmer"><strong>"HMMER"</strong>
Preferences</a> tab allows you to configure locally installed HMMER tools.
</li>
structure information read from PDB will be processed and annotation
added to associated sequences.
<p>
- <em>Use RNAView for secondary structure</em> - if selected, the
- pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
- will be called to derive secondary structure information for RNA
- chains.
- <p>
<em>Add secondary structure annotation to alignment</em> - if
selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
implementation DSSP</a> will be used to add annotation to polypeptide
the backbone atoms in the PDB file will be extracted as annotation
lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
<p>
- <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
+ <em><strong>Default structure viewer</strong></em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
viewing 3D structures.
<p>
<em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
installed the chosen viewer in a non-standard location, you can specify it
here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
<p>
+ <em>Sequence <-> Structure Mapping Method</em> - This setting controls whether
+ Jalview attempts to retrieve mappings between Uniprot protein
+ sequences and 3D structures in the PDBe with SIFTS, or constructs a
+ mapping by conservative alignment between the sequences and chains
+ in the 3D structure data using the Needleman and Wunsch algorithm.
+ SIFTS is enabled by default.
+ <p>
<em>PDB Fields shown in Search and Structure Summaries</em> - ticks
in this table indicate fields shown by default when browsing results
of a free text search via the PDB sequence fetcher, or 3D structures
<em>Sort with New Tree</em> - When selected, any trees calculated or
loaded onto the alignment will automatically sort the alignment.
</p>
- <p>
+ <p> </p>
+ <p>
+ <a name="startup"><strong>Startup</strong></a>
+ </p>
+ <p>
+ When Jalview is launched it by default examines the available memory
+ and requests up to 90% to be allocated to the application, or 32G,
+ which ever is smaller. The <em>Startup</em> tab allows you to adjust
+ the maximum percentage and hard limits for Jalview memory allocation
+ stored in your .jalview_properties file.
+ </p>
+ <p> </p>
+ <p>
<a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
</p>
<p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),