• 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.

Developers

Wilma Olson

Xiang-Jun Lu

Categories

X-ray Crystallography

Structure Analysis

Structure Visualization

Nucleic Acids

Versions

• Linux 32: 2.1b-20130222
• Linux 64: 2.1b-20130222
• OSX Intel: 2.1b-20130222
• OSX PPC: 2.0
• SGI Irix: 1.5

Citations

Xiang-Jun Lu and Wilma K Olson (2008) "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures." Nature Protocols, 3, 1213-1227.

• an extension to Molscript

Developers

Robert Esnouf

Categories

Structure Visualization

Versions

• Linux 32: 2.6b
• Linux 64: 2.6b
• OSX Intel: 2.6b
• OSX PPC: 2.6b
• SGI Irix: 2.6b

Citations

Esnouf, R. M. (1999) Acta Crystallographica, D55, 938-940.
Esnouf, R. M. (1997) Journal of Molecular Graphics, 15, 132-134.
Kraulis, P. J. (1991) Journal of Applied Crystallography, 24, 946-950.

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

Developers

Liz Potterton

Stuart McNicholas

Categories

Structure Visualization

Versions

• Linux 32: 2.7.3
• Linux 64: 2.7.3
• OSX Intel: 2.7.3
• OSX PPC: 2.1.0

Citations

Potterton et al. Developments in the CCP4 molecular-graphics project. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 12 Pt 1) pp. 2288-94

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

Developers

Thomas Goddard

Greg Couch

Tom Ferrin

Categories

Structure Visualization

Versions

• Linux 32: 1.6.2
• Linux 64: 1.6.2
• OSX Intel: 1.6.2
• OSX PPC: 1.4.1
• SGI Irix: 1.170

Citations

Pettersen et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) vol. 25 (13) pp. 1605-12

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

Developers

Michael Lappe

Categories

Structure Analysis

Structure Visualization

Versions

• Linux 32: 1.1rc6
• Linux 64: 1.1rc6
• OSX Intel: 1.1rc6

Citations

Vehlow et al. CMView: interactive contact map visualization and analysis. Bioinformatics (2011) vol. 27 (11) pp. 1573-4

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

Developers

Dino Support

Ansgar Philippsen

Categories

Structure Visualization

Versions

• Linux 32: 0.9.4
• Linux 64: 0.9.4a
• OSX Intel: 0.9.4
• OSX PPC: 0.9.0
• SGI Irix: 0.9.0

Citations

How to reference DINO:
If a figure is produced with DINO, please cite either underneath the figure itself, as a standalone reference, or in Materials and Methods (usually items i and iii are the best choice):

(i) underneath Figure Figure created with DINO (http://www.dino3.org)

(ii) as reference Figure created with DINO#

Ansgar Philippsen, http://www.dino3d.org

(iii) in Material and Methods [...] Figures #, # and # were created using DINO (http://www.dino3d.org).

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

Developers

Espript Info

Xavier ROBERT

Categories

Structure Analysis

Structure Visualization

Versions

• Linux 32: 2.3
• Linux 64: 2.3
• OSX Intel: 2.3

Citations

Gouet et al. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic acids research (2003) vol. 31 (13) pp. 3320-3

Gouet et al. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics (Oxford, England) (1999) vol. 15 (4) pp. 305-8

• 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.

  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.

  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.

  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.

Developers

Michael Sanner

Arthur Olson

Categories

Structure Visualization

Utilities

Versions

• Linux 32: 1.5.6rc3
• Linux 64: 1.5.6rc3
• OSX Intel: 1.5.6rc3
• OSX PPC: 1.5.4

Citations

ADT: Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod. 1999. 17:57-61.

isocontour: Bajaj et al. Fast IsoContouring for Improved Interactivity, Proceedings of ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, 1996, pages 39 - 46, San Francisco, CA

msms: Sanner et al. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 1996. 38(3):305-320.

PCVolRen: Bajaj et al. A Parallel Multi-PC Volume Rendering System, ICES and CS Technical Report, University of Texas, 2002.

Pmv: Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod. 1999. 17:57-61.

vision: Sanner et al. ViPEr a Visual Programming Environment for Python. 10th International Python Conference, February 2002.

• 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.
  

Developers

Bradley Smith

John Badger

Categories

X-ray Crystallography

Structure Visualization

Versions

• Linux 32: 2010.10
• Linux 64: 2010.10

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

Developers

Sharron Thomas

Kurt Wuthrich

Categories

Structure Visualization

Versions

• Linux 32: 2k.2.0
• Linux 64: 2k.2.0
• OSX Intel: 2k.2.0
• OSX PPC: 2k.2.0
• SGI Irix: 2k.1.0

Citations

Koradi et al. MOLMOL: a program for display and analysis of macromolecular structures. Journal of molecular graphics (1996) vol. 14 (1) pp. 51-5, 29-32

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

Developers

Per Kraulis

Categories

Structure Visualization

Versions

• Linux 32: 2.1.2
• Linux 64: 2.1.2
• OSX Intel: 2.1.2
• OSX PPC: 2.1.2
• SGI Irix: 2.1.2

Citations

Per J. Kraulis, "MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950.

Technical Notes

OpenGL enable molscript is the default. The following aliases have been set to use a povray enabled version:

molscript-pov

molauto-pov

More information about the povray enabled version can be found here:

http://www.stanford.edu/~fenn/povscript/

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

Developers

Luca Jovine

Categories

Structure Visualization

Nucleic Acids

Versions

• Linux 32: 1.5.2
• Linux 64: 1.5.2
• OSX Intel: 1.5.2
• OSX PPC: 1.5.2
• SGI Irix: 1.5

Citations

There is no paper describing nuccyl (yet). However, if you found the program useful and would like to mention it in your publications together with PyMOL, you could use an URL citation of the type:

Jovine, L. nuccyl (2003) http://www.biosci.ki.se/groups/ljo/software/nuccyl.html

• 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).

Developers

Kalle Gehring

Christophe Deprez

Categories

Structure Visualization

Versions

• Linux 32: 1.82
• Linux 64: 1.82
• OSX Intel: 1.82

Citations

Deprez et al. Solution structure of the E.coli TolA C-terminal domain reveals conformational changes upon binding to the phage g3p N-terminal domain. Journal of molecular biology (2005) vol. 346 (4) pp. 1047-57

• 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.

Categories

Structure Visualization

Versions

• Linux 32: 1.5.0.4
• Linux 64: 1.5.0.4
• OSX Intel: 1.5.0.4
• OSX PPC: 1.2r2
• SGI Irix: 0.99

Citations

The PyMOL Molecular Graphics System, Version 1.2r3pre, Schödinger, LLC.

Technical Notes

Pymol is installed with the APBS plugin. Your PDB must be in the following format:

1. No water or ligand molecules
2. B-factors < 100
3. No alternative conformations
4. No partial occupancies

• 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.

Developers

RasMol Developer Group

Categories

Structure Visualization

Versions

• Linux 32: 2.7.5.2
• Linux 64: 2.7.5.2
• OSX Intel: 2.7.5.2
• OSX PPC: 2.7.4.2

Citations

Sayle and Milner-White. RASMOL: biomolecular graphics for all. Trends Biochem Sci (1995) vol. 20 (9) pp. 374

Bernstein. Recent changes to RasMol, recombining the variants. Trends Biochem Sci (2000) vol. 25 (9) pp. 453-5

Goodsell. Representing structural information with RasMol. Curr Protoc Bioinformatics (2005) vol. Chapter 5 pp. Unit 5.4

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

Developers

Ethan Merritt

Categories

Structure Visualization

Versions

• Linux 32: 3.0
• Linux 64: 3.0
• OSX Intel: 3.0
• OSX PPC: 2.7d
• SGI Irix: 2.6e

Citations

Merritt and Bacon. Raster3D: photorealistic molecular graphics. Meth Enzymol (1997) vol. 277 pp. 505-24

Merritt and Murphy. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr (1994) vol. 50 (Pt 6) pp. 869-73

• a popular molecular graphics software display package.

Developers

Mike Carson

Categories

Structure Visualization

Versions

• Linux 32: 3.32
• Linux 64: 3.32
• OSX Intel: 3.5
• OSX PPC: 3.5
• SGI Irix: 3.2

Citations

Carson. Ribbons. Meth Enzymol (1997) vol. 277 pp. 493-505

Technical Notes

Ribbons is supported on Fedora Core releases 3 and lower and Fedora releases 7 and higher. Due to significant library compatibility issues, ribbons is not supported on Fedora Core 4 through 6.

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

Developers

VMD Developer Team

Categories

Structure Visualization

Versions

• Linux 32: 1.9.1
• Linux 64: 1.9.1
• OSX Intel: 1.9.1
• OSX PPC: 1.8.7
• SGI Irix: 1.7.1

Citations

Humphrey et al. VMD - Visual Molecular Dynamics. J. Molec. Graphics. 1996. 14: 33-38. For a list of other citations go to: http://www.ks.uiuc.edu/Research/vmd/allversions/citations/

Technical Notes

Condensed “movie making tips” from VMD. The main points:

1. Just load 1 frame for every 1ns of simulation time. A 1 us simulation would only need 1000 frames. The “stride” feature in the VMD trajectory loader dialog lets you set this (e.g. to 20, if the generated frames are at a rate of 50 ps per frame). Make sure you choose “load all frames at once”, rather than “background”. The “background” option will render frames as they’re loaded.

2. Figure out what region you want to “fix” in the structure. Get the residue IDs for this. Go to Extensions→Analysis→RMSD Tool and enter “protein and resid START to STOP”, then click on “Align”. This will align the entire structure through all frames and have resids START to STOP as stationary as possible.

3. Use “Create Rep” to create multiple representations of the structure. The selection box can be used to specify what you want to show. “protein and resid START1 to STOP1 START2 to STOP2 …” is a common entry. “water and within 3 of protein” would show all water molecules within 3A of an atom associated with a protein. You can then play with the different kinds of views (coloring, style, transparency) for each representation individually.

4. Clicking on a representation will show or hide it.

5. For each representation, set the Trajectory to smooth over several frames. I have found that a 4ns smoothing window reduces the jitter without eliminating interesting side chain motion. YMMV.

6. Set Display→Rendermode→GLSL to do OpenGL/CUDA rendering. This should make a big difference. I haven't done a formal test of this, but my laptop, with 48 CUDA 3 processing cores, seems to do much better, smoother, and faster rendering than my Mac Pro (which does not have a compatible CUDA card).

Movie Making:

• loaded every 20th frame (about 1000 from 20k) * smoothing window of 4  * internal Tachyon ray tracer  * image smoothing on  * half size reduction * 30 FPS (NTSC) * MPEG output

Apparently a good trick to get nice looking animations is to double therendering window then set the movie generator to half-size the result. I guess this gives a “per-frame” image smoothing effect as thepotentially hard edged rendered image is reduced to an anti-aliased frame.