incorporating secondary structure assignments from PDB file

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

NO_GRAPH Icons ||E,B1|E|E|E|||

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.


J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764