X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;h=5a3fe7aabb0f3d93d8b419748b15a64fc0dad07d;hb=214ad7e089fdf9cde66ac5e5d56d498101bbe2c3;hp=5fda2dfcbf2ba3abb28758f13d7589eb5725fd61;hpb=28a1247c88a7cc31a836da99a1d795072ca543a7;p=jalview.git
diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 5fda2df..5a3fe7a 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -222,17 +222,15 @@
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.
PDB Fields shown in Search and Structure Summaries - ticks in this table indicate fields shown by default when browsing results @@ -249,11 +247,33 @@ 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