[Tutor] Basic web form interaction with http://propka.ki.ku.dk/

Troels Emtekær Linnet tlinnet at gmail.com
Sat Aug 6 16:44:32 CEST 2011

Hi Mateus.

No, I was certainly not aware of BioPython. What a nice project. I will
check it out.

No, the script should not download a .pdb file.
The idea is, that a "researcher/student" sits with his/hers favorite protein
in pymol and would like to know the pKa value
of his/hers favorite amino acids.

The student "probably" has only pymol installed, and would not like to
install to many other python packages.
Maybe the student can't, because it is a university computer.

With this web-interaction script, the students activate the script, with:
get_pka Molecule, residue

The script saves the molecule to a .pdb file. Interact with the propka web
site, send the file, wait 1 minute, grep for the line
with the amino acid, and parse it back to pymol, so the student can see the

To big benefit with this, is that the student does not have to handle to
hard installations of scripts/programs or the manual way.
And the student knows, that the pKa prediction is from the newest software
If the student get greedy, he/she starts writing a pymol script that alter
the pdb structure in pymol, and receive the new pKa value for each
structural change.
The downside, is of course the "waiting" time for the server response.


Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752

2011/8/6 Mateusz Koryciński <mat.korycinski at gmail.com>

> Hi,
> Have You tried something similar to interface used in BioPython? I think U
> could get solution by reading code for connection with databases like
> Entrez. Maybe this will give you some ideas.
> Do you want your script to download pdb file from PDB database? Or you want
> only sending and receiving from propka?
> Cheers,
> Mateusz
> 2011/8/6 Troels Emtekær Linnet <tlinnet at gmail.com>
>> Dear Python users.
>> I am an semi-experienced in python, but totally new on the web
>> interactions.
>> I have been working with scripts o the protein program Pymol, which can be
>> extended with python script.
>> I hope that some of you can help me with an interaction script to
>> http://propka.ki.ku.dk/.
>> I hope that some of you can show be a basic python script to load the
>> suitable python modules and interacting
>> with the web form.
>> The main idea is, to load a protein structure in pymol.
>> Then writing a pymol/python script that saves the stucture of the protein
>> into a .pdb file.
>> Then open http://propka.ki.ku.dk/, send the .pdb file, wait 1-2 minutes
>> for the result, and capture the result.
>> I hope that some of you can show be the basics steps, to interact with the
>> web form.
>> Best
>> Troels
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> --
> Pozdrawiam,
> Mateusz Koryciński
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