Hi Ezequiel, thanks for your mail.
I'm working with a protein domain composed by two chains (due to a
proteolytic processing). Jalview associates the chain A from the PDB,
but no the chain B, i.e only the N-terminal of the sequence. How to
can be associate the C-terminal with the chain B? Thanks in advance
You've hit a limitation with the way Jalview currently handles sequence-structure associations. The algorithm for mapping sequences to structures picks the single highest scoring match between each sequence and structure, rather than the optimal cover for mapping structure onto sequence.
There's a workaround - but it is a bit of a kludge. In the structure->Associate PDB ID menu, you can enter a PDB ID which jalview will then fetch. If the PDB ID has more than four symbols, then Jalview assumes the 5th symbol is a chain code, and will only consider that chain when mapping that sequence to the structure.
So - for example:
You have an alignment containing a sequence which combines chain A and B of PDB entry 1GAQ.
1. use the manual 'associate PDB ID' menu entry from the structure->Associate Structure with Sequence-> Enter PDB ID submenu to add both '1GAQA' and '1GAQB' as PDB ID associations for that sequence.
2. Select the Structure->View Structure->1GAQA - jalview will download and view the structure as normal, with chain A associated.
3. Select View Structure->1GAQB - Jalview will ask you if you want to download and superimpose the structure for 1GAQB in the view of 1GAQA - say yes here, and both chains will now be displayed and associated.
As you can see, this work around is by no means perfect, and I've created an Improvement request on Jalview's bug tracker:
It might also be possible to put together a groovy script to add the additional chain mapping - but the best solution is to improve the sequence/structure association algorithm. Is this something you need urgently ?
On Sun Mar 10 02:48:41 2013, Ezequiel Noguera wrote:
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