Structure Visualization

SBGrid supports 18 structure visualization software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

3DNA

- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.

yes yes yes

BOBSCRIPT

- an extension to Molscript

yes yes yes

CCP4mg

- offers a quick and easy way to create beautiful publication quality images and movies and to superpose and analyze structures.

yes yes yes

Chimera

- a highly extensible, interactive molecular graphics program, often a tool of choice for rendering EM volumes.

yes yes yes

CMView

- an interactive contact map visualization and analysis tool that supports assessing similarities and differences between structure- or contact predictions.

yes yes yes

DINO

- a realtime 3D visualization program for structural biology data.

yes yes yes

ESPript

- (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences and coordinate files.

yes yes yes

MGLTools

- a software package comprised of AutoDockTools (adt), Python Molecule Viewer (pmv) and a python programming environment called Vision. Developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. <p> AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. <p> PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering. <p> Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

yes yes yes

MIFit

- an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed by Bradley Smith as an Open Source project while working for Rigaku/MSC Inc. A particular focus of the MIFit software is the efficient solution and analysis of protein:ligand complexes.

yes yes

MOLMOL

- a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules.

yes yes yes

MolScript

MolScript is one of the most popular programs for the generation of publication-quality figures.

yes yes yes

NUCCYL

- a Perl program that allows PyMOL to display atomic models of nucleic acids in a highly simplified representation.

yes yes yes

ProtSkin

- converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).

yes yes yes

PyMOL

- widely used molecular visualization package developed by Warren DeLano, and now maintained by Schödinger, LLC. SBGrid non-profit laboratories have full access to the official incentive builds of PyMOL. The SBGrid Consortium PyMOL license credentials are contained in the NOTES file in the PyMOL installation directories in your software installation.

yes yes yes

Rasmol

- a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

yes yes yes

Raster3D

- a set of tools for generating high quality raster images of proteins or other molecules.

yes yes yes

Ribbons

- a popular molecular graphics software display package.

yes yes yes

VMD

- a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

yes yes yes