Protein structure features

Jalview Discussion
1

Hello there,

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just a quick note to say that I am using Jalview for annotating
structural features of proteins using my own feature files. The kinds of
things that I am annotating include interactions with small molecules as
extracted from Credo
(http://www3.interscience.wiley.com/journal/121654603/abstract). Jalview
has proven a very useful tool for doing this kind of thing. It did take
a little while to get my first feature file accepted by the program
because of the lack of error messages. Also, I need to replace
disordered residues with X's so that the residue numbers match the
sequence numbers. That said, my co-workers seem to to find the results
useful.

Cheers,

Will

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Dr Will Pitt
Visiting Research Associate
Cambridge University
Department of Biochemistry
80 Tennis Court Road
Cambridge
CB2 1GA
UK

44(0)1223 766031

2

Hi Will.

Glad to hear that Jalview has been useful here - annotation is one of
its primary uses, so its great to get some feedback.

William Ross Pitt wrote:

has proven a very useful tool for doing this kind of thing. It did take
a little while to get my first feature file accepted by the program
because of the lack of error messages.

I understand your point here - error messages are output to the console,
but of course - they should be reported in a dialog box, and should be a
little more informative.

Also, I need to replace

disordered residues with X's so that the residue numbers match the
sequence numbers.

Ok. Perhaps we should talk more off list about this. It sounds like you
need to work with UNIPROT sequences directly rather than import the
sequences directly from the PDB file (in which case, only residues with
an alpha carbon will be used to construct the sequence).

That said, my co-workers seem to to find the results

useful.

Great!

Thanks
Jim.

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