[Jalview-discuss] fetch of multiple PDB sequences

[James Procter]

Hi Maria.

The PDB viewer in Jalview 2.4 does keep track of mappings between a
sequence and a structure, but it ignores the SEQRES entry, and instead
extracts the sequence directly from the residues in the alpha carbon
trace (i.e. the displayed sequence only contains residues with an alpha
carbon ATOM entry). In the 2ZETA case, you'll notice that the displayed
sequence around the loop is :

 >PDB|2ZET|2ZET|A/57-60
 GASG

If you mouse over this region, the PDBRESNUM feature labels give the PDB
residue number field and insertion code for each residue's corresponding
CA ATOM entry, but these values are not used to map features.

Unfortunately, although this isn't perfect for everyone, there are no
plans (currently) to change this behaviour - but I think there is a
workaround for you.

It sounds like what you really want to do is to import the uniprot
sequences associated with each structure. This means the alignment
viewer contains the full sequence, and the CA-trace sequences of any
structures will be aligned to this, so features in the uniprot
coordinate system are properly located on the structure. If you don't
have the uniprot IDs handy, then have a look at PICR
(www.ebi.ac.uk/Tools/picr) which you can use to lookup the uniprot IDs
that cross-reference the structures you want to view.

I hope this helps.
Jim.

Maria Luisa Rodrigues wrote:
> Hi Jim,
> 
> I'm using the PDB fetcher option, which is really nice, but I've noticed
> that it is not able to cope with missing residues in the structure. It
> seems that the program reads the number of the first residue of a chain
> and then it numbers all other residues accordingly to that. For
> instance, since residues 59-61 of 2ZET chain A (Rab27b proten) are
> missing in the structure (I think they should have been included in the
> model with high B factors...) Jalview numbered Rab27b Ser62 as Ser59!
> This caused an error in the sequence feature annotation.
> I am doing something wrong?

> Thanks again,
> 
> Luisa


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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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