[Jalview-discuss] feature request: display secondary structure of known structures

[Jim Procter]

  Hi Thomas - thanks very much for this feature request (and the kind 
words). I've added it to our issue tracker here: 
http://issues.jalview.org/browse/JAL-674

In principle, its possible to retrieve secondary structure annotation 
via DAS - there's a server that will return annotation for every PDB 
code. There are a couple of points where the information flow needs to 
be joined up in order to get this to happen automatically for any 
sequence (e.g. retrieve secondary structure for any uniprot sequence 
with PDB cross references). Watch the comments on this feature request 
for workarounds and updates.

Jim.

On 06/10/2010 12:15, Thomas Evangelidis wrote:
> Dear developers,
>
> may I request to add an option that can display the secondary
> structure elements (SSEs) of every sequence with known structure below
> (or above) the alignment? In conjunction with secondary structure
> prediction by Jpred, the user could adjust the alignment to eliminate
> disruption of SSEs in the unknown sequences. With this feature Jalview
> could become the ultimate commercial free alignment editor for
> comparative modeling.
>
> best regards,
> Thomas
>
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