Re: r11106 - /branches/bieri_gui/gui_bieri/analyses/auto_rx_base.py -- April 28, 2010 - 00:50

I like the tree view idea. Do you think of a a collection of amino acids 
(dna, rna...) that is initially linked to the sequence or should the 
entries be read from the pdb file.

I also think reading sequence from pdb file is by far the best and most 
appropriate method! This will never get disabled. Maybe, we should 
introduce a correction function that converts (or adjusts) assignments 
to the pdb file, if the assignment was not done with the same numbering?

Cheers

Edward d'Auvergne wrote:
> On 28 April 2010 00:13, Michael Bieri <michael.bieri@xxxxxxxxxxxxx> wrote:
>   
> > Yes, I think we should make a dialog that already displays the sequence,
> > so the users are able to see if the sequence is correctly read in. I
> > will add this element at a later step.
> >     
>
> This would be good for a future version.  What do you think of that
> tree view GUI element to display the hierarchical structure?  This
> could be placed in its own class so that it can be reused inside a
> frame/window in the future, so that you click on the spin and all the
> info is displayed in another GUI element next to it.
>
>
>   
> > What do you think? I even would prefer to have a text box, where users
> > can paste a sequence in, such as in CcpNmr.
> >     
>
> Users are fussy and have their own way of doing things.  Why have the
> sequence typed out if you can read it directly from a PDB file?  We
> shouldn't artificially restrict user's abilities as the philosophy
> behind the design of relax is flexibility, which hopefully can be
> transported into the GUI.  Pasting a sequence in would be quite useful
> for some users.  But if you would like this to be the only choice,
> you'll first have to write the sequence data for this thing
> http://en.wikipedia.org/wiki/Paclitaxel ;)  Anyway, any way of loading
> the sequence data will be accepted into the core of relax and can
> accessed via any UI element - that would just add more flexibility
> which is a good thing.  I do think that reading the sequence from PDB,
> a specific columnar formatted sequence file (can be any data file
> which contains the sequence info in certain columns), or pasted
> sequence data should all be accessible as ways of filling the
> molecule-residue-spin data container structure.  Just don't forget the
> RNA/DNA/sugar/small molecule people - you never know, you might be
> working on one of these (maybe complexed with a protein) in the
> future!
>
> Regards,
>
> Edward
>
>
>