By Sergio Decherchi In Scripts and Utilities 243 downloads
This utility is a minimal Graphical User Interface to NanoShaper to get the visualization of a molecule surface; it should not be considered a substitute for advanced tools such as VMD. For this script to work Enthought python must be used and optionally togetherwith Prody installed. Put in the .\NSgui folder the NanoShaper executable and run NSgui.py. This minimal GUI allows to dowload or load a pdb file, apply Amber99 radii using DelPhi .siz file format, define a configuration file for NanoShaper and display the 3D surface together with, if requested, the cavities. The integration with Prody allows to filter out the interested part of the protein using the familiar selection string of VMD. By default the surface is shown in non transparent mode. To allow transparency and see cavities enable "Cavity Detection" and "Save Status Map" on the configuration settings.