GUI Web

From PropKaWiki

PropKa GUI

   Release 5
         - What's new:
              • Separate option for initializing PROPKA 3.1 calculations
              • Alternative pka values of coupled ionizable residues can be considered and recalculated (with PROPKA 3.1)
              • Missing ligand atoms contributing to the pKa shift of terminal amino acids with non-ionizable side chains have been corrected
              • Formatted reading of PROPKA3 output file (for large residue IDs) 
         - Download the GUI in the binary or Windows format (Last Updated: Sept 21st, 2011)
         - Installation Notes (General)
         - If necessary, follow installation instructions for Mac, Linux and Windows users
         - In order to configure the GUI to be able to execute the PROPKA calculations locally, please follow these intructions.

   Release 4
         - Release Notes
         - Download the GUI in the binary or Windows format (Last Updated: May 31st, 2011)
         - Installation Notes (General)
           - If necessary, follow installation instructions for Mac, Linux and Windows users
         - Screencast tutorial
         - Manual
         - In order to configure the GUI to be able to execute the PROPKA calculations locally, please follow these intructions.
         - Tips on using the GUI and known problems 
         - Upgrade: The users who have installed previous release of the PropKa GUI can upgrade it by replacing 
           the old propka.tcl file with the new one in the propka1.1 plugin directory. 
           No more modifications are required.
 
         Important!
         Filename pattern for saving PDB and PROPKA output file to load this data into the GUI for the new PROPKA 3 has been changed!
         To work with the new output files save a PDB file as ABCD.pdb (where ABCD is a PDB code) and a pKa file as ABCD.pka . 
            This is the default extension pattern for saving PROPKA3 output files both for the PROPKA web server and for local PROPKA3 calculations.
         For using previous PROPKA2, please keep the old pattern which is ABCD.pdb and ABCD.pdb.pka for PDB and pKa file, respectively. 

About

PropKa GUI is a TCL plugin for the Visual Molecular Dynamics (VMD) software available here.

Please cite this reference in publications:

• Michal Rostkowski, Mats H.M. Olsson, Chresten R. Sondergaard and Jan H. Jensen: "Graphical analysis of pH-dependent properties of proteins predicted using PROPKA"BMC Structural Biology, 2011, 11:6.

(Please report errors to "michal _at_ chem.ku.dk".)

Here is a short introduction.