Editing Propka (section)

=== Known bugs ===
* Bonds can be multiplied from amino acids to Ligands like ZN or ATP. Assume the shortest bond to be correct.
*# ZN: This is caused, since ZN has no ID number and when there are several in the same chain. This can be reproduced for 1HP1, bond: A41ZNCC. Here it shows to bonds, where only the shortes is correct. No fix possible.
*# ATP: This is caused, since propka sometimes eats the ending of the atom name. In the .pdb file is written O3', which propka represents like O3. Therefore a wildcard "*" is generel inserted, which can cause multiple bonds to the ATP molecule. This can be reproduced for 1HP1, bond: A504ATPSH. Here multiple bonds are made to all the O3*,O2* atoms. No fix possible.
* The propka server sometimes use another naming scheme for Ligands. These Ligands will not be pka labelled or shown in pymol. The results will still downloaded to "/.Results_propka/file.pka"
*# This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG. 
* Alternative configurations of a Ligand is at the moment a problem, and will not be shown. For example 1HXB and the ligand ROC. 
*: The script extraxt AROC and BROC from pymol, which does match with ROC in the .pka file. Try save the protein with only one configuration of the Ligand. 
** >In pymol:
**: fetch 1hxb, async=0
**: create 1hxbA, 1hxb and not alt B
**: save 1hxbA.pdb, 1hxbA
** >Quit pymol
** >Manually replace with text editor in .pdb file "AROC" with " ROC"  Remember the space " "!
** >Then in pymol
**: load 1hxbA.pdb
**: import propka
**: propka verbose=yes



[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Pymol-script-repo]]