[Jalview-discuss] Re: incorporating secondary structure assignments from PDB file

[James Procter]

Hi Michael.

I've taken the liberty of ccing my reply to the Jalview discussion list, 
in case there is anyone out there who might be able to help you out with 
a script.

Michael Sawaya wrote:
> Is there a way to load secondary structure symbols into jalview
> from the HELIX and SHEET records in a PDB file?
This can easily be implemented in Jalview, but it is one of those 
features that never quite got to the top of the pile for actually 
implementing. If you are (or know) a java programmer then I can give you 
some instructions about where to start if you like (and we can then 
incorporate it into the main Jalview source tree).

> If not, what is the easiest way to create the helix and sheet
> symbols in jalview given a known structure?
In principle the secondary structure records from PDB structures are 
also available via uniprot DAS annotion - but this results in sequence 
features rather than the helix and sheet glyph annotation.

> Do I have to edit a annotation file with nomenclature such as this?
> 
> NO_GRAPH    Icons     ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
This is the easiest way of doing it if you are preparing these files 
from a script.  You can also attach annotation to a particular sequence 
(see http://www.jalview.org/help/html/features/annotationsFormat.html):
 >myPDB
ADFQFQA

SEQUENCE_REF	myPDB
NO_GRAPH	Icons	||E,B1|E|E|E|||
SEQUENCE_REF	ALIGNMENT

Otherwise, you can trace (there ought to be a jalview command to do this 
automatically) the sheet and helix annotation for a sequence as a new 
annotation row (but this can't be associated with a particular sequence 
from within the gui).

thanks for your email, and I hope this doesn't cause you too much 
inconvenience. Its unfortunate that there aren't quite enough hours in 
the day for implementing all the features we'd like!

Happy Jalviewing
Jim Procter.

-- 
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J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk