PDB secondary structure import

Hi,

I was wondering if someone could tell me if it is now possible to display the secondary structure information from the header of a protein pdb file imported as a pdb file into Jalview 2.8.

Preferably as both diagrammatic annotation and sequence colouring.

I can get the colouring in the associated Jmol structure just fine, but is there a way of getting this information into the sequence alignment for one of the sequences?

I can appreciate translating the information from the pdb header may be difficult.

CHEERS!

Michael

The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902.

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Hi there, Michael.

I've been out of action for a bit, otherwise I'd have sent a reply earlier.

I was wondering if someone could tell me if it is now possible to display the secondary structure information from the header of a protein pdb file imported as a pdb file into Jalview 2.8.

Preferably as both diagrammatic annotation and sequence colouring.

In the current version of jalview, the only way you can get secondary structure annotation is if your pdb file's secondary structure information is available from the DSSP das service, or - if the sequences in it have a Uniprot ID, from the Uniprot database reference fetcher.

I can get the colouring in the associated Jmol structure just fine, but is there a way of getting this information into the sequence alignment for one of the sequences?

Sadly not in this version of Jalview - but the new 'sequence associated colouring' feature in v2.8 will provide a mechanism for linked Jmol->Jalview colouring in the future.

I'm also pleased to say that we had a summer student this year working on including RNA secondary structure annotation in Jalview - I've been tidying up her work and in the process, hooked up Jmol's own DSSP implementation to get secondary structure annotation directly from PDB files imported to Jalview. The code is still rough and ready, but should be available from the development build in the very near future, and we'll put up a news item about it too, so watch the site for updates.

Jim.

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On 28/11/2012 12:51, michael wilson wrote: