Hi Mateus.<br><br>No, I was certainly not aware of BioPython. What a nice project. I will check it out.<br><br>No, the script should not download a .pdb file.<br>The idea is, that a "researcher/student" sits with his/hers favorite protein in pymol and would like to know the pKa value<br>
of his/hers favorite amino acids.<br><br>The student "probably" has only pymol installed, and would not like to install to many other python packages. <br>Maybe the student can't, because it is a university computer.<br>
<br>With this web-interaction script, the students activate the script, with:<br>get_pka Molecule, residue<br><br>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<br>
with the amino acid, and parse it back to pymol, so the student can see the pKa.<br><br>To big benefit with this, is that the student does not have to handle to hard installations of scripts/programs or the manual way.<br>
And the student knows, that the pKa prediction is from the newest software available.<br>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<br>
structural change.<br>The downside, is of course the "waiting" time for the server response.<br><br>Best<br>Troels<br><br><br clear="all"><br>Troels Emtekær Linnet<br>
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<br><br><div class="gmail_quote">2011/8/6 Mateusz Koryciński <span dir="ltr"><<a href="mailto:mat.korycinski@gmail.com">mat.korycinski@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<font size="2"><font face="arial,helvetica,sans-serif">Hi,<br></font></font><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">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.<br>
</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Do you want your script to download pdb file from PDB database? Or you want only sending and receiving from propka?</font></div>
<div><div class="gmail_quote"><br></div><div class="gmail_quote"><br></div><div class="gmail_quote">Cheers,</div><div class="gmail_quote">Mateusz</div><div class="gmail_quote"><br></div><div class="gmail_quote"><div class="im">
2011/8/6 Troels Emtekær Linnet <span dir="ltr"><<a href="mailto:tlinnet@gmail.com" target="_blank">tlinnet@gmail.com</a>></span><br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">Dear Python users.<br><br>I am an semi-experienced in python, but totally new on the web interactions.<br>
</div>I have been working with scripts o the protein program Pymol, which can be extended with python script.<div class="im"><br>
<br>I hope that some of you can help me with an interaction script to <a href="http://propka.ki.ku.dk/" target="_blank">http://propka.ki.ku.dk/</a>.<br>
I hope that some of you can show be a basic python script to load the suitable python modules and interacting<br>with the web form.<br><br>The main idea is, to load a protein structure in pymol. <br>Then writing a pymol/python script that saves the stucture of the protein into a .pdb file.<br>
Then open <a href="http://propka.ki.ku.dk/" target="_blank">http://propka.ki.ku.dk/</a>, send the .pdb file, wait 1-2 minutes for the result, and capture the result.<br><br>I hope that some of you can show be the basics steps, to interact with the web form.<br>
<br>Best<br><font color="#888888">Troels<br>
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<br></blockquote></div><br><br clear="all"><br>-- <br><span style="font-family: verdana,sans-serif;">Pozdrawiam,</span><br style="font-family: verdana,sans-serif;"><font color="#888888"><span style="font-family: verdana,sans-serif;">Mateusz Koryciński</span><br>
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