X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;h=0ae0684e52451afc90d4ef0a6449c63b91d8ac47;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=41dae1df61dad3e5469daedd1d1766e1c60607c5;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git
diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 41dae1d..0ae0684 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -225,17 +225,15 @@
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
@@ -252,11 +250,33 @@
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:
+
+ - No proxy servers will configure Jalview to use a
+ direct internet connection.
+ - System proxy servers will configure Jalview to use
+ the proxy server passed to it by your system at startup.
+ - Use these proxy servers: allows you to set a custom
+ proxy server.
+
+ If you normally use a proxy server for using the internet, you must
+ choose one of System proxy servers, or if these have not been
+ passed correctly you should set your own proxy servers to use by selecting
+ Use these proxy servers.
+ 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.
+ 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.
+ You can also check the Authentication required box if your proxy
+ requires username and password authentication. You can enter both the
+ Username and Password but only the Username will
+ be stored in Jalview's preferences file, the password will only be stored
+ until the end of the current Jalview session.
+ This means that if the proxy settings are still valid, Jalview will ask for
+ the password when it starts the next session.
Usage statistics, Questionnaire and Version checks