Overview

RasMol is a molecular graphics program for displaying macromolecules in three dimensions. RasMol renders each atom in a macromolecule in its specified 3-D position according to the data in an atomic coordinate file, adding the appropriate covalent bonds. The program also interprets data about atom identities, secondary structure, disulfide bridges, hydrogen bonding, polypeptide chains, and more, if present in the coordinate file. RasMol is unequaled in its ability to rotate smoothly a space-filled macromolecule in three dimensions. Simple combinations of mouse and keyboard allow you to rotate, move, and zoom the molecule in 3-D. Drop-down menus allow you to change color, display, and more. RasMol also accepts a large vocabulary of commands, providing the savvy user with almost unlimited control over the display. One drawback to RasMol is that a user must learn this specialized command language to tap the majority of the program's power. Another limitation is that RasMol, while excellent for self-directed exploration by a knowledgeable user, is quite limited as a presentation tool and can be troublesome for beginners. Despite these limitations, RasMol remains a popular and very powerful molecular visualization tool.

How Long Did It Take to Learn to Use It Productively?

I have been using RasMol for over three years, and I'm still learning new tricks. It is an extremely powerful program that utilizes a combination of mouse operations, simple menus, and a complex command vocabulary. Learning the mouse and menus takes very little time (less than one hour), but their use is limited; learning the command language can take weeks or months, but provides complete control over the 3-D structure. To get the most out of RasMol, you must learn at least some of the command language. As a result, RasMol does not get high marks for ease of use.

RasMol has a straightforward, two-window interface. The main window displays the 3D structure; it also contains the menus. The command-line window is where you type the commands; it also shows information about the structure and feedback from command entries. The mouse operations are very straightforward, and quickly become second nature. Most of the menus are likewise intuitive (though some are a bit cryptic). Many of the commands, too, are not difficult to figure out; for example, Background White or Spacefill On. Others, such as Set Picking Monitor, are more cryptic.

Product Quality

Customizability

RasMol is open-source, which means that the source code is available for use or modification at no cost (although not without restrictions). Three-D structure files for a vast (and growing) number of macromolecules can be obtained freely from the Protein Data Bank, and there are a number of other good repositories of more specialized structures on the Internet. Finally, there are very few restrictions on how you can display a 3-D structure in RasMol; it is an extremely powerful program.

Ability to Program in Scripts, Add Extension Modules, etc.

RasMol has the ability to read two different types of script files. The first type, RasMol-saved scripts, are saved directly from RasMol for later display using the Save Script command. The second type, external scripts, are text files that contain RasMol commands. These are useful for common, widely applicable tasks that normally require multiple command entries (for example, rendering some "default" view of a macromolecule).

Ability to Import and Export in Different File Formats

RasMol 2.7 can read Protein Data Bank (PDB), Mol2, Mol (from MDL), XYZ (XMol), CHARMM, CIF, and mmCIF structure files. It can write raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile, MolScript input script, Kinemage, RasMol script (.SPT), or PDB files.

Useful or Unusual Features

RasMol provides unparalleled control over the display of a 3-D structure. You can open a large file (e.g., a multisubunit protein), select a part of the structure (e.g., one subunit), and save it as a new structure file. You can save a particular view as a script file and open it later. RasMol reads most common structure file formats, as well as RasMol-saved scripts and text files that contain RasMol commands (external scripts). It can print the current view (72 dpi), or export it as a common image file (PICT, GIF).

It is the command language that makes RasMol so powerful. To cite a few examples: the Within command allows you to select atoms that lie inside a user-defined radius around some user-defined target - for example, all protein atoms within hydrogen-bonding distance of a ligand. RasMol will instantly calculate and display the distance between two atoms (Monitor). You can select combinations of atoms using complex Boolean modifiers and primitive expressions, and then define this set with a keyword for easy reference. You can also use one of RasMol's three dozen or so predefined sets (protein, nucleic, solvent, hydrophobic, helix, side chain, etc.). Color atoms using common names (white, red, blue, etc.) or exact RGB triplets; slab to see the interior of a solid structure; visualize hydrogen bonds or disulfide bridges; and much more.

I found only three significant differences between the PC and Macintosh versions of RasMol 2.7. First, several of the mouse-keyboard combinations on the PC utilize the right mouse button, which is absent from the standard Macintosh mouse (the control key is usually used instead). Second, I found that manipulating a structure was not as smooth in 2.7 as it was in 2.6 on the Macintosh; I did not see this difference between versions on the PC. Finally, when PC RasMol is launched, its command window is minimized by default (available from the taskbar).

Limitations

The main limitation to RasMol is its large and complex command language. On one hand, it gives the knowledgeable user complete control over how the program renders a macromolecule; on the other hand, it makes it prohibitively difficult for beginners to tap into much of this power. In addition, although it is possible to save a particular view for later use, the process is cumbersome and prone to error, and may jeopardize many hours of work. In RasMol, the industry-standard keystroke/menu option (command-S on the Macintosh) saves the current molecule as a PDB file, which does not include any display information. This should be changed so that the default save option is a script file. Finally, the safest way to use RasMol (and sometimes the only way) is to have all files in the same directory or folder. RasMol-saved script files include an absolute directory path to the relevant structure file. If either file is moved, the script will not work. RasMol would benefit by being more savvy about file locations, or at least degrade gracefully (for example, by providing an option to browse to a structure file that is not in its original location). Unlike Chime, RasMol does not support true animation, which limits its utility as a presentation tool.

Comparisons with Similar Software

For the savvy user, RasMol is one of the most powerful molecular visualization programs, and certainly the most powerful free program, available today. Its 3-D rendering algorithm is outstanding, and is the foundation for several other popular programs, including WebLab Viewer and Chime. The main disadvantage to RasMol is its extensive command language, which makes it more difficult to use than other programs in this class. RasMol 2.7 has some useful features missing from earlier versions, including a help section, support for additional languages and platforms, new labeling features, more colors, support for multiple-model nuclear magnetic resonance files, and more. However, many of the improvements in 2.7 benefit the knowledgeable user but do not improve the learning curve. To give RasMol truly mainstream appeal, its command-line input should be replaced by a graphic interface (menus, toolbars, etc.).

Technical Support and Documentation

RasMol, as a product of a grassroots community effort, has no official technical support. However, the Molecular Visualization Freeware Email List (aka the RasMol Email List), is an excellent source of information and help. Responses are rapid and helpful, and it is the rare question that goes unanswered. There are several RasMol manuals available on the Internet that explain most or all of the RasMol commands; these can be downloaded easily and at no cost. RasMol 2.7 also includes a help feature.

Target Users

Anyone with an interest in structural biology will find RasMol an useful tool, and well worth the effort of learning its language. In addition, since structure is intimately tied to function, and macromolecules pervade science disciplines in general, RasMol can be put to good use almost anywhere in science. Typical RasMol users range from protein crystallographers to science educators to high school students.