VASCo
Description
VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions. Crystal contacts and biological contacts can be calculated based on surface points. Molecular properties such as electrostatic potential or hydrophobicity can be calculated and mapped on those surface points. The molecular surfaces and properties are calculated using existing established programs, which are integrated into the package, as well as using own developed programs. The modular pipeline can easily be extended to include new properties for annotation. The output of this pipeline is most conveniently displayed in PyMOL as Compiled Graphics Objects (CGO) using a custom-made plug-in.
License
The software is available only to academic, government, and other nonprofit institutions for noncommercial, nonprofit internal research purposes. Details about license can be found at official site.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of vasco and load default version of vasco as
module avail vasco/ # list available modules module load vasco # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail vasco
and choose explicit version you want to use.
VASCo.py -h
Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.
VASCo can be added as plugin to PyMOL application - script used for this kind of set up can be found at /software/vasco/1.0.2/ppixplugin_v077.py.
Documentation
http://genome.tugraz.at/VASCo/vasco_documentation.shtml