This program allows to patch DelPhi 77 double precision version to support NanoShaper and the CUDA Solver

This script loads a .off file and visualize it. By default the surface is semi-transparent in order to see cavities. If the cavities loading is enabled, grid points in cavities are shown together with a scalar indicating the ratio of the cavity volume and the volume of the water molecule approximated as a sphere with a radius of 1.4 Angstrom. By indicating the name of the NanoShaper executable both computation and visualization can be done in one single command.

msms_redirect.cpp : this file is used to allow full VMD visualization of the surface. This program redirects VMD to the two saved files triangulatedSurf.off.vert, triangulatedSurf.off.face. This redirect is used because VMD is not able to enable all surface visualization features when a saved file is loaded; that is a specific VMD program path has to be used. If you load an MSMS external file, surface effects cannot be applied. In order to get a proper visualization the following steps must be followed:

1) Compile msms_redirect, call it MSMS and put it into the VMD folder

2) Start VMD, load your pdb file and request for MSMS surface: this will generate the file atoms.xyzr

3) Feed atoms.xyzr to NanoShaper to get the desired mesh

4) Convert the .off file together with atoms.xyzr in MSMS format by off2msms.py.

5) Name the two files as triangulatedSurf.off.vert, triangulatedSurf.off.face, and copy them on VMD folder

6) Request again to VMD the MSMS surface. The surface computed by NanoShaper should be visualized.

At this last point VMD will run msms_redirect that will copy the two desired files triangulatedSurf.off.vert, triangulatedSurf.off.face into the temporary files that VMD 'believes' are from MSMS. At this stage you will get the raw surface together with proper atom info (if provided). It is up to the user to grant the consistency of the pdb loaded in VMD and the .xyzr file provided to the off2msms.py script.

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.

This script converts a "name.off" file into the pair "name.off.vert" and "name.off.face" MSMS files. If also an optional xyzr file (coordinates+radius) file is provided then for each vertex the nearest atom is found and it is saved into the MSMS file. This allows to load the files into VMD and have all the info needed for surface per-atom colouring. Note that when VMD loads an externally computed surface it does not load all the information but only the raw triangulated surface. In order to correctly load all the info a trick is needed (see msms_redirect).

This script loads a .off triangulated mesh and build several files: the .idtf file converted mesh, the .u3d file that represents the mesh, the latex file that properly embeds the mesh, the final pdf in which the the mesh is embedded. The script assumes that a idtf -> u3d converter is available: for easiness of using a converter in the \bin folder is given. The script also assumes that pdflatex is available (here an example pdf); in order to get the final pdf the movie15 package is requested, for this reason this file is included. For example for Windows the execution string is:

This script reads an .off triangulated mesh and adds the grey color to the vertices. The converted file can be visualized using .off VMD plugin. This script can be used to get a fast way to visualize the surface on VMD. For a full featured visualization on VMD msms_redirect should be used.

This script reads an .off file and performs scaling and zero centering of the mesh. This is useful when an arbitrary mesh is loaded inside NanoShaper: the mesh scale must be of the same order of molecular surfaces in order to get consistent results.

This utility converts a pdb into a xyzr file using the file amber.siz. This file is in DelPhi radii format and contains Amber99 radii. This script requires the excellent ProDy package; this can be downloaded here.

This Python script allows you to convert an Amber (version 7 and higher), topology file (.prmtop) into a pqr format. This script takes as input the pdb of the system, the prmtop file, the output pqr file name and, optionally, a VMD-like atom selection string. To parse the pdb and apply the selection the ProDy package is used and must be previously installed: ProDy is an excellent tool to manipulate MD trajectories and pdb files and can be dowloaded from http://www.csb.pitt.edu/prody.

The script typical application is in converting a system used in a MD simulation to perform computations with DelPhi or protonate a system by tleap (AmberTools) and then using DelPhi on it.The presence of the atom selection string allows the user to remove in one step all the undesired components of the system (e.g. waters).

A typical usage example is:

python getPQRfromPrmtop.py sys.pdb box.prmtop sys_prot.pqr "protein"

where "protein" is the VMD-like atom selection string to remove all but the protein atoms. Another useful example to retain protein atoms, DNA atoms and those belonging to the ligand LIG is:

python getPQRfromPrmtop.py sys.pdb box.prmtop sys_dna_lig.pqr "protein or nucleic or resname LIG"

This script shows as red dots the projected boundary grid points (a set of points) passed as a file.