Peptide Builder

Development
1

I’m finishing up a peptide builder extension. I have the code which
generates the peptide, but I’m curious about the interface.

I’m thinking there should be a text box for typing a sequence, plus a
grid of buttons which add text to the box (e.g., buttons “arg”, "gly,"
etc.) So far, I’ve assumed that the grid of button should be organized
alphabetically for the 20 standard amino acids. But I looked at
Spartan, which organized them by frequency of residue in the PDB. (At
least that’s my assumption. “Gly” was very early.)

Now which is more intuitive? I’d go for the alphabetical. Right?

Any complaints?
-Geoff

2

IMO, alphabetically is better.

On Wed, May 20, 2009 at 3:18 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

I’m finishing up a peptide builder extension. I have the code which
generates the peptide, but I’m curious about the interface.

I’m thinking there should be a text box for typing a sequence, plus a
grid of buttons which add text to the box (e.g., buttons “arg”, “gly,”
etc.) So far, I’ve assumed that the grid of button should be organized
alphabetically for the 20 standard amino acids. But I looked at
Spartan, which organized them by frequency of residue in the PDB. (At
least that’s my assumption. “Gly” was very early.)

Now which is more intuitive? I’d go for the alphabetical. Right?

Any complaints?
-Geoff

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3

Am Mittwoch, den 20.05.2009, 09:18 -0400 schrieb Geoffrey Hutchison:

I’m finishing up a peptide builder extension. I have the code which
generates the peptide, but I’m curious about the interface.

Now which is more intuitive? I’d go for the alphabetical. Right?

I have a different suggestion (as an alternative, perhaps the layout
could be changed by a QComboBox).
I would also go for the alphabetical order as default and also offer
these two:

– 1 –
Neural / Hydrophobic / hydrophil

http://www.egbeck.de/skripten/bilder/!aminoac.gif

– 2 –

Polar / non polar / acidic / basic

http://www.chempage.de/theorie/amino.jpg

Both are quite common in biology and biochemistrybook like the Stryer,
the Lenninger, Purves or Campbell.

Carsten

4

On May 21, 2009, at 7:00 AM, Carsten Niehaus wrote:

I have a different suggestion (as an alternative, perhaps the layout
could be changed by a QComboBox).

I don’t think that’s a good idea. I don’t like interfaces that move
buttons, IMHO.

I would also go for the alphabetical order as default and also offer
these two:
…
Neural / Hydrophobic / hydrophil
…
Polar / non polar / acidic / basic

So we have “Color by residue” which can set colors based on these
schemes. Check it out. If it doesn’t meet your needs, it’s easy to add
another color scheme or three.

Cheers,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/