- Gap Colour - 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. -
-"Structure" Preferences tab added in Jalview 2.8.2
@@ -215,11 +213,6 @@ structure information read from PDB will be processed and annotation added to associated sequences.- Use RNAView for secondary structure - if selected, the - pyRNA RNAView service (https://github.com/fjossinet/PyRNA) - will be called to derive secondary structure information for RNA - chains. -
Add secondary structure annotation to alignment - if
selected, Jmol's
implementation DSSP will be used to add annotation to polypeptide
@@ -228,16 +221,27 @@
Add Temperature Factor annotation to alignment - 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.
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.
- Default structure viewer - choose Jmol or CHIMERA for + Default structure viewer - choose Jmol, CHIMERA, CHIMERAX or PYMOL for viewing 3D structures.
- Path to Chimera program - 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.
+ Path to Chimera/X/Pymol program - 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.
For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also double-click this field to open a file chooser dialog.
+ Sequence <-> Structure Mapping Method - 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. +
+ PDB Fields shown in Search and Structure Summaries - 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.
"Connections" Preferences tab @@ -249,11 +253,33 @@ browser application.
- Proxy Server
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.
+ Proxy Server
+ There are three settings to choose from:
+
Usage statistics, Questionnaire and Version checks
@@ -264,6 +290,22 @@
statement for more information.
+ The "Backups" Preferences Tab +
+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.
++ Schemes - select from three default schemes Single Backup, Keep All Versions, and Rolled Backup Files, or choose Custom to enable a previously defined custom scheme. +
+ Custom - Check this box to adjust the parameters of the currently selected scheme. Once OK is selected these parameters will be saved as the Custom scheme in your user preferences. To revert changes hit Cancel. +
+Scheme Examples - shows how backup files will appear according to the currently selected scheme and parameters. +
+Deleting Old Backup Files - these settings control how many backups are kept.
+Backup filename strategy - specify the naming convention for numbered backups and how they are ordered.
+ @@ -383,6 +425,21 @@ loaded onto the alignment will automatically sort the alignment.+
+ Startup +
++ 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 Startup tab allows you to adjust + the maximum percentage and hard limits for Jalview memory allocation + stored in your .jalview_properties file. +
++ Web Services Preferences - documentation for this tab is + given in the + Web Services + Preferences section.