Editing Propka (section)

== Changelog ==
* 20111202
*# This code has been put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].

* 20110823
*# Fixed some issues with selection algebra of Ligands.
*# Now colors Ligands automatically to purple scheme.

* 20110822
*# Made the naming scheme consistent, so one can work with multiple proteins, and the grouping still works.
*# Bonds to N-terminal and C-terminal did not show up. Fixed.
*# If one just write "propka", the "last" molecule in the pymol object list is now assumed, instead of the first. This makes mutagenesis analysis easier.
*# The pka difference from assumed standard values are now also displayed. Standard values are set to: pkadictio = {'ASP':3.9, 'GLU':4.3, 'ARG':12.0, 'LYS':10.5, 'HIS':6.0, 'CYS':8.3, 'TYR':10.1}
*# The menu size is made bigger, so it can fit the long names for the bonding partners. There's also a slider that you can drag using the mouse
*#:--it's the tiny tab between the command line and the movie controls. Drag that left or right.

* 20110821
*# The resn function was made wrong, only taking the last item of list. Fixed.
*# resn= can now also be print to screen/log for ligands like ATP. Ex: resn=CYS.ATP.TRP
*# Ligands are now also written to the "stripped-file". "./Results_propka/PDB.stripped"
*# Bonds are now also made for Ligands.

* 20110820
*# If one points to a result .pka file, then "method" is automatically set to "method=file".
*# Added the ability for pka values for ligands
*# Bonds are now generated for the pka atoms.
*# The color scheme is changed from "rainbow" to "red_white_blue". This is easier to interpret.
** CC: COULOMBIC INTERACTION. Color is red.
** SH: SIDECHAIN HYDROGEN BOND. Color is brightorange.
** BH: BACKBONE HYDROGEN BOND. Color is lightorange.

* 20110817
*# If just invoking with "propka", it will select the first molecule. And now it is possible also to write. "propka all".
*# Removed the "raise UserWarning" if the script is oudated. Only a warning message is printed.

* 20110816
*# Made the execution of the pymol command script silent, by only using cmd.API. This will raise a Warning, which can be ignored.
*# Built-in a Script version control, to inform the user if the propka script is updated on this page
*# The alternate attribute for the labeling atoms are reset. It was found pymol objected altering names for atoms which had alternate positions/values.
*# Reorganized the input order, which means that: molecule=all is default.

=== 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]]