Editing Propka (section)

=== Examples ===
Read about the proteins here:<br>
http://www.proteopedia.org/wiki/index.php/4ins <br>
http://www.proteopedia.org/wiki/index.php/1hp1 <br>

<syntaxhighlight lang="python">
import propka

fetch 4ins, async=0
propka        OR
propka 4ins   OR
propka 4ins, resi=19.20, resn=ASP.TYR, logtime=_, verbose=yes

import propka
fetch 1hp1, async=0
propka molecule=1hp1, chain=A, resi=305-308.513, resn=CYS, logtime=_

import propka
getpropka source=ID, PDBID=4ins, logtime=_, server_wait=3.0, verbose=yes, showresult=yes
</syntaxhighlight>

<gallery heights="240px" widths="340px">
Image:Propka1HP1.png|propka used on 1HP1.
Image:Propka1HP1-ATP.png|propka used on 1HP1, zoom on ATP ligand.
Image:Propka1HP1-ZN.png|propka used on 1HP1, zoom on ZN ligand metal center.
</gallery>
<gallery heights="240px" widths="340px">
Image:Propka4INS.png|propka used on 4INS.
Image:Pymolpropkamenu.png|The easy menu does it easy to click on/off ligands and bonds
Image:Resultslog.png|An appending logfile ./Results_propka/_Results.log saves the input commands and the result for the residues specified with resi= and resn=
</gallery>

pka atoms are created and renamed for their pka value. That makes it easy to "click" the atom in pymol and instantly see the pka value.

The atoms b value are also altered to the pka value, and the atoms are then spectrum colored from pka=0-14. 

The pka value of 99.9 represent a di-sulphide bond, and is colored gold and the sphere size is set a little bigger. 

If one wants to see the specified result, the logfile ./Results_propka/_Results.log saves the link to the propka server. Here one can see in an interactive Jmol appp, the interactions to the pka residues.