Hello Jordan - thanks for your email.
Jordan Willis wrote:
I know there is a feature where I can select my sequence and
have jnet give me back the predictions(which is actually not working at the moment for me).
Ah. There was a problem with the JNet web service, which was recently upgraded; this has now been fixed.
I was wondering if you could add other secondary
structure predictions or
There aren't any other secondary structure prediction services available to Jalview at the moment, but this will change in the future.
known secondary structure elements to your list as well, like from the pdb heading.
Jalview doesn't parse the secondary structure from PDB files, but we are open to code contributions from anyone who'd like to implement this.
However, if you want to view secondary structure assignments for structures available in the PDB then you can import them using the sequence fetcher, and then use the DSSP das source to retrieve the secondary structure assignments.
> And is using jnet the only ss predictor I can
use that could give a graphical output?
The JNet server is - as far as we are aware - the only one that creates annotation in a form that Jalview can visualise. However, there is no reason why the output of other servers couldn't be parsed into annotation - the annotations file (http://www.jalview.org/help/html/features/annotationsFormat.html ) can be used to create any number of labels, protein secondary structure symbols, graphs and histograms below the alignment.
'hope this helps!
Jim.
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