</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="../webServices/webServicesPrefs.html"><strong>"Web
Service"</strong> Preferences</a> tab allows you to configure the <a
href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
overview that are hidden in the alignment.
</p>
<p>
- <em>Gap Colour</em> - The default colour scheme for a new alignment
- window. If the chosen option is "User Defined" then the
- last User Defined Colour loaded or saved via the User Defined
- Colours panel will be loaded.
- </p>
- <p>
<a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
</p>
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
<em>Add Temperature Factor annotation to alignment</em> - if
selected, values extracted from the Temperature Factor column for
the backbone atoms in the PDB file will be extracted as annotation
- lines shown on the alignment.
+ 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 or CHIMERA for
+ <em><strong>Default structure viewer</strong></em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
viewing 3D structures.
<p>
- <em>Path to Chimera program</em> - Optional, as Jalview will search
- standard installation paths for Windows, Linux or MacOS. If you have
- installed Chimera in a non-standard location, you can specify it
- here, by entering the full path to the Chimera executable program.
- Double-click this field to open a file chooser dialog.
+ <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
+ standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have
+ 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
+ offered by the 3D Structure Chooser.<p>
<p>
<a name="connections"><strong>"Connections"
Preferences tab</strong></a>
browser application.
</p>
<p>
- <em>Proxy Server</em><br> If you normally use a proxy server
- for using the internet, you must tick the box "Use a Proxy
- Server" and enter the address and port details as necessary.
+ <em>Proxy Server</em><br>
+ There are three settings to choose from:<br>
+ <ul>
+ <li><em>No proxy servers</em> will configure Jalview to use a
+ direct internet connection.</li>
+ <li><em>System proxy servers</em> will configure Jalview to use
+ the proxy server passed to it by your system at startup.</li>
+ <li><em>Use these proxy servers:</em> allows you to set a custom
+ proxy server.</li>
+ </ul>
+ If you normally use a proxy server for using the internet, you must
+ choose one of <em>System proxy servers</em>, or if these have not been
+ passed correctly you should set your own proxy servers to use by selecting
+ <em>Use these proxy servers</em>.
+ You will then need to enter the host and port details as necessary.
Web Services will not work if you are using a proxy server and do
- not enter the settings here.
+ not choose the system proxy or enter your own settings here.<br>
+ There are separate host and port settings for HTTP and HTTPS proxies.
+ Often these are the same but you should enter the host and port into both
+ rows.<br>
+ You can also check the <em>Authentication required</em> box if your proxy
+ requires username and password authentication. You can enter both the
+ <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
+ be stored in Jalview's preferences file, the password will only be stored
+ until the end of the current Jalview session.<br>
+ This means that if the proxy settings are still valid, Jalview will ask for
+ the password when it starts the next session.
</p>
<p>
<em>Usage statistics, Questionnaire and Version checks</em><br>
statement</a> for more information.
</p>
<p>
+ <a name="backups"><strong>The "Backups" Preferences Tab</strong></a>
+ </p>
+ <p>Since Jalview 2.11.0, overwriting an existing file when saving
+ or exporting data will by default trigger a backup file to be
+ created. Several options are provided to control how backup files
+ are named, and how many old versions will be kept.</p>
+ <p>
+ <em>Schemes</em> - select from three default schemes <em>Single Backup</em>, <em>Keep All Versions</em>, and <em>Rolled Backup Files</em>, or choose <em>Custom</em> to enable a previously defined custom scheme.
+ </p><p>
+ <em>Custom</em> - Check this box to adjust the parameters of the currently selected scheme. Once <em>OK</em> is selected these parameters will be saved as the <em>Custom</em> scheme in your user preferences. To revert changes hit <em>Cancel</em>.
+ </p>
+ <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters.
+ </p>
+ <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
+ <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p>
+ <p>
<a name="links"><strong>The "Links" Preferences
tab</strong></a>
</p>
loaded onto the alignment will automatically sort the alignment.
</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>
+ <em>Web Services Preferences</em> - documentation for this tab is
+ given in the
+ <a href="../webServices/webServicesPrefs.html">Web Services
+ Preferences section</a>.
<p> </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff