From 2eeea2f43d7bbaafd79ebd4185b42fc60646d9e3 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 14 Aug 2006 11:08:54 +0000 Subject: [PATCH] 2.1 updates --- help/html/features/hiddenRegions.html | 32 +++++++++++++++++++++++++++++- help/html/features/viewingpdbs.html | 35 ++++++++++++++++++--------------- help/html/menus/alwcalculate.html | 1 - help/html/menus/alwedit.html | 1 - help/html/whatsNew.html | 2 +- 5 files changed, 51 insertions(+), 20 deletions(-) diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index d1dc5f0..511d80e 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -1,6 +1,36 @@ Hidden Regions -Now you see them, now you dont +

Hidden Regions

+

To hide selected sequences from an alignment, use the "View + -> Hide -> Selected Sequences" menu item or simply select "Hide + Sequences" from the Popup menu after a right click on the sequence Ids. +

+

Hidden sequences will not be used in any calculations, editing or web service + alignments performed on visible sequences.

+

A more advanced hide involves a right-mouse click on a sequence, then selecting + "SequenceID -> Represent Group with SequenceId". Using this method + of hiding sequences, any edits performed on the visible group representative + will be propogated to all the sequences in that group.
+ The hidden sequences will not be used in any calculations or web service alignments. +

+

 

+

To hide selected columns from an alignment, use the "View + -> Hide -> Selected Columns" menu item, or right click within a region + of selected columns in the scale above the alignment (only available in non + wrapped mode) and select "Hide Columns".

+

Hidden columns will not be used in any calculations. This allows you to eg. + create trees from the visible alignment and ignore any poorly aligned sections + of the alignment, without cutting and deleting them permanently from your alignment.
+ It is possible to retrieve the input data to any trees, PCA analysis windows + which were created from alignments containing hidden columns by using the "File + -> Input Data..." menu item from the tree window.

+

Editing the alignment is bound by the hidden columns, ie you cannot move residues + across a hidden column boundary.

+

Any web service alignments performed on sequences which contain hidden columns + send the alignment as a series of chunks delimited by the hidden columns.

+

 

+

 

+

 

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 2890b5d..ef222b1 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -7,23 +7,26 @@ accessed via the "Sequence→View PDB entry:" entry from the sequence's pop-up menu.

-

There are two ways to associate PDB files with sequences:

+

To associate PDB files with a sequence, right click on a sequence ID and select + "Associate Structure with Sequence", and one of the submenus:

-For help on viewing and colouring structures see the PDB Viewer help page. -

+

Note: You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this + service are automatically associated with their source database entry. For PDB + sequences, simply select PDB as the database and enter your known PDB id (appended + with ':' and a chain code, if desired).

+

For help on viewing and colouring structures see the PDB Viewer help page.

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 5a97296..ed5de39 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -3,7 +3,6 @@

Alignment Window Calculate Menu

-Calculate