From: Jim Procter Date: Tue, 17 Sep 2024 15:56:03 +0000 (+0100) Subject: JAL-4418 documentation for ss annotation row preference and auto show (JAL-4425 JAL... X-Git-Tag: Release_2_11_4_0~4^2~6 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=157385223801346ee6800b5eb1e0cecc33b12701;p=jalview.git JAL-4418 documentation for ss annotation row preference and auto show (JAL-4425 JAL-4392) --- diff --git a/help/help/html/calculations/protssconsensus.html b/help/help/html/calculations/protssconsensus.html index b98fb14..76619db 100755 --- a/help/help/html/calculations/protssconsensus.html +++ b/help/help/html/calculations/protssconsensus.html @@ -31,9 +31,12 @@ secondary structure for an alignment of protein sequences where one or more sequences have secondary structure annotation, in the same way as is done with the sequence consensus.

-

Secondary structure consensus rows will only be shown if - there are secondary structure data available for two or more - sequences in the alignment.

+

To view secondary structure consensus rows, you should first + enable the Secondary Structure checkbox in + Jalview + Preferences. Once this option is checked, a consensus row will + be shown if secondary structure annotations are available for + two or more sequences in the alignment.

Sources of secondary structure data

Sequences can have several different secondary structure diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html index 6708c57..943118e 100755 --- a/help/help/html/features/preferences.html +++ b/help/help/html/features/preferences.html @@ -95,7 +95,12 @@ standard annotations Conservation, Quality, Occupancy and Consensus for the alignment may be shown or hidden by default using the checkboxes adjacent and - below. + below.
Secondary Structure + consensus annotation rows can also be enabled + (since version 2.11.4.0). When enabled, + secondary + structure consensus rows only be shown if there are secondary + structure annotions on the alignment.

Show group: Conservation and Consensus controls the display