Color by secondary structure


Is it possible to color every sequence in an alignment by experimental secondary structure for those sequences that have structures in the PDB?

Can I do this automatically or alternatively, can I import a file of secondary structure assignments (that I can create) that would indicate what residues to color in each sequence? I want to color each sequence differently according to whatever its secondary structure is in its experimental structure.

It would be terrific if Jalview could look up structures in the PDB (which it currently does) and then color the sequence in the alignment by the experimental secondary structure annotated in the PDB files.




Roland Dunbrack
Professor, Institute for Cancer Research
Fox Chase Cancer Center
Philadelphia PA 19111

Hi Roland & Vivek… (& jalview discuss!)

As Geoff says - please use the development build for this. We are just about to freeze the version for release, so it’s “nearly” bug free! Please also follow Mungo’s advice about configuring secondary structure processing in the ‘Structures’ preferences pane.

From what you said in the last email, I think you shouldn’t need to rename the sequences in your alignment. However, there are a few ways you might add your preferred structures:

  1. If you don’t have too many structures, then I’d recommend you just manually pick them for each sequence via the structure chooser dialog:
  • import the alignment, select all the sequences, right-click on the ID panel and select the ‘View 3D Structure…’ option. Then for each sequence, manually pick the entry you prefer. Once you’re ready, hit ‘View’ and Jalview will download Uniprot records for each sequence and map the structures, before opening the structures in your configured viewer.

This way, Jalview will by default use SIFTs to correctly map structures to Uniprot sequences, which may be important for some of the coordinate data you want to view on the alignment. Once the mapping has finished, just close the structure view, and the annotation will remain (we may well provide an additional button next release that avoids opening the viewer completely!).

  1. If you have lots of structures, and you don’t necessarily need SIFTS mappings, then I’d recommend creating a set of structures named according to the Uniprot ID, selecting all the files and dropping them onto the alignment. Jalview will then prompt you about matching up the files to each sequence - which will result in annotation being added. It’s a little cumbersome, but the quickest way at the moment. If you later want to open these structures, you can select them via the ‘Cached PDB Files’ drop down menu option on the Structure Chooser.

  2. If you have lots of sequence/structure mappings to make and want SIFTS mappings, then we can provide a groovy script you can use to associate and add the structure annotations.

As Geoff mentioned, we’re interested in making these kinds of operations easier to perform. Also, the PDB structure selection UI is still very new, so we’d love to hear your thoughts on how it could be improved !

Let us know how you get on…


PS. A final tip. Once you have secondary structure annotation on a sequence, it stays with it when you create a new alignment - just select ‘Add reference annotation’ from the Selection and sequence ID popup menu.

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