GUI Web
From PropKaWiki
!!! NEW !!!
PropKa GUI is now available in a standard VMD distribution (since version 1.9.1)!
Release 6
- Screencast tutorial for the interface overview
- Manual (To be updated), documentation for the previous release is available here.
- Brief description of new features can be found in Tips.
- In order to configure the GUI to execute PROPKA calculations locally, please follow these intructions.
- Manual installation / upgrade
- Download the GUI in the binary or Windows format (Last Updated: Jan 27th, 2012)
- Installation Notes (General)
- If necessary, follow installation instructions for Mac, Linux and Windows users
- 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.
- Tips on using the GUI and known problems.
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. |
