Editing Propka (section)

== Introduction ==
This script can fetch the pka values for a protein from the [http://propka.ki.ku.dk/ propka] server. The "propka" function downloads the results and processes them. <br />
It also automatically writes a pymol command file and let pymol execute it. This command file make pka atoms, rename them, label them and color them according to the pka value.

If you put the mechanize folder and the propka.py script somewhere in your pymol search path, then getting the pka values is made super easy. By the way, did you know, that you don't have to prepare the .pdb file by adding/removing hydrogens? The [http://propka.ki.ku.dk/ propka] server uses its own internal hydrogen placement algorithm.

<syntaxhighlight lang="python">
import propka
fetch 4ins, async=0
propka
</syntaxhighlight>

If there is no web connection, it is possible to process a result file from a previous run or from a downloaded propka webpage result. This can be a handsome feature in a teaching/seminar situation, since it speeds up the pymol result or that an available web connection can be doubtful. Just point to the .pka file: Remember the dot "." which means "current directory".
<syntaxhighlight lang="python">
import propka
load 4ins.pdb
propka pkafile=./Results_propka/4ins"LOGTIME".pka, resi=18.25-30, resn=cys
</syntaxhighlight>

The last possibility, is just to ask for the pka values of a recognized PDB id. This is done with the "getpropka" function.
<syntaxhighlight lang="python">
import propka
getpropka source=ID, PDBID=4ake, logtime=_, showresult=yes
</syntaxhighlight>