VMD

[VMD] "is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer."

Type of Data

Unsurprisingly, most respondents use this software for molecular/atomic/protein visualisation.

Size of Data Set

This varies widely. About half the respondents have data sets smaller than a few GB. Two had data sets of 40 and 50 GB. Otherwise they had 1,000 or 30,000 atoms.

Advantages

The most widely cited advantages are

• quality of output
• range of supported file types
• simple to use/script

Quality of Documentation/Tutorials

Documentation was almost universally regarded as good or very good. One respondent stated it was difficult to navigate.

Range of Data Formats

Again, almost universally regarded as good, with two exceptions:

• "temperamental with periodic images"
• "no support for cif"

Level of Support Available

A range of resources is used: mailing lists and online forum.

Performance

Performance generally regarded as good, especially on a desktop machine.

Limitations

• "Needs a good graphics card"
• "TCL scripting is limited"
• "Slow to load large data sets"
• "Some additional analysis tools are unstable"
• "Some representations not appropriate for periodic boundary conditions"
• "Cannot interpret bond types"

Comments

The tools are free and open source