Protein Explorer vs. RasMol
by Eric Martz, August 29, 2000; revised July 2002

The goal of Protein Explorer is to enable you to focus on the science, not the software. Chime adds a great deal of power to RasMol, but using the full power of either program requires advanced technical knowledge and a lot of time -- hence their power is inaccessible to most of the people who could benefit from it. The goal of Protein Explorer is to make the power of Chime accessible to students, educators, and scientists. More is available about the evolution of the uses of Chime and the purpose of Protein Explorer.

Version 2.0 of Protein Explorer, released in increments in 2000-2002, is much easier to use, and much more powerful than RasMol. Because Chime is available only for Windows and Macintosh, Protein Explorer runs best on those platforms; however, there are several methods for getting it to work on linux, or other platforms.

The list below is not meant in any way to disparage RasMol! Without RasMol, there would be no Protein Explorer, because it requires Chime, which in turn is built using RasMol's source code! Protein Explorer is possible only because of the brilliant infrastructure contributed by Roger Sayle, the author of RasMol.

Novice Features
Advanced Features
For graphic evidence of the user-friendliness and power of Protein Explorer, see the snapshots.

Novice Features

  1. Protein Explorer's first image of any molecule is maximally informative. RasMol's first image is wireframe, of very little use for macromolecules. This is by design, to force the user to initiate exploration, but it leaves you "on your own".

  2. Protein Explorer's first image is accompanied by FirstView, a description of the image and how to interpret it, with additional layers of in-depth help available through hyperlinks. These provide illustrated introductions to computer renderings of backbone traces, disulfide bonds, water, ligands and the color schemes employed. Basic uses of Chime are explained (such as clicking on any atom to identify it, and rotating by dragging with the mouse). RasMol provides no assistance with interpretation, and no explanation is automatically displayed concurrently. You are simply "on your own" in RasMol.

  3. Clicking on an atom identifies clearly its element, residue name, sequence number, and atom serial number. The latter two numbers, in particular, aren't clearly distinguished in RasMol's terse one-line identification report.

  4. Protein Explorer's QuickViews menus follow the RasMol paradigm (select, then render, then color) but have powerful options not on RasMol's menus. In fact, RasMol has no select menu at all (except "Select All") -- in RasMol, all selections must be done with commands.

      The QuickViews SELECT menu includes:
    1. Protein or Nucleic (with a one-click distinction between DNA and RNA)
    2. Individual chains
    3. Secondary structure elements (helices, sheets)
    4. Backbone, Sidechain
    5. Solvent, Ligand
    6. Hydrogen
    7. Invert selection
    8. Range of residues or any arbitrary residues (with Seq3D)
    9. Select atoms, residues, or chains by clicking on them.

      QuickViews' DISPLAY menu includes in addition to the more useful renderings on RasMol's Display menu:

    10. Trace (smoothed backbone)
    11. Vine (smoothed backbone with sidechains)
    12. Hbonds, SSBonds
    13. Dots
    14. Solvent accessible surface (with toggle for solid vs. transparent)
    15. Cation-Pi interactions
    16. Salt bridges
    17. Contact surface (overview of noncovalent bonds between any two moieties)
    18. Only (hide not selected)
    19. Hide selected
    20. Center (all selected atoms, or clicked atom)
    21. Clicked atoms: distances, monitor lines, angles, dihedrals, labels (with form slot to enter label text)

      QuickViews' COLOR menu includes in addition to the more useful color schemes on RasMol's Colours menu:

    22. Polarty (2, 3 or 5 colors): hydrophobic vs. polar vs. charged.
    23. ACGTU scheme for reading the code from nucleotide strands.
    24. A series of plain colors (red, white, etc.)

      You rarely need the powerful but confusingly-organized menus of Chime when using Protein Explorer. When you do (as for selecting all tryptophans) detailed instructions are provided.

    25. When a menu selection is made in QuickViews, context-triggered help with color keys (for color scheme selections), and troubleshooting information appear automatically. RasMol offers only a reference manual that must be invoked with commands such as "help cpk", and has no built-in color keys in color.

    26. Protein Explorer has convenience buttons to toggle continuous slow spinning**, visibility of water or ligands, slab and stereo, as well as buttons to zoom up or down, change between white and black background, center any atom, or reset the initial view. RasMol has no continuous automatic spinning capability, and no convenience buttons.

    27. When a new center of rotation is specified, it also remains in the center of the screen during zooming**. In RasMol, it often zooms out of view.

    28. Protein Explorer has a molecule information window accessible at all times, with direct links to the PDB file header and RCSB Structure Explorer for the PDB ID code currently loaded, as well as links to external resources for viewing specific oligomers, fewer or single chains, evolutionary rate (ConSurf), and information about crystal contacts and model quality. RasMol offers no such help.

    29. Protein Explorer will display the amino acid (or nucleotide) sequences for all chains in a readable one-letter code. Touching any residue shows the sequence number and three-letter code. Any desired amino acids (such as all cysteines) can be highlighted in color for easy spotting. Gaps and insertions are shown clearly, as is the length of each chain. RasMol's sequence display is three-letter code only, plain text, not interactive, no help provided.  

    30. Protein Explorer's sequence-to-structure interface, Seq3D highlights (and selects) any amino acids or ranges of amino acids (or nucleotides) when they are clicked in the sequence listing.

    31. When a multiple-model PDB file (NMR result) is loaded, only the first model is shown in FirstView and QuickViews. Upon entering QuickViews, you are alerted that there are multiple models, and the model count is shown in the QuickView help frame along with additional information about how to view the other models. By default, RasMol does not inform you that you are looking at a multiple model file, and shows only the first model. If you know the proper command, you can get RasMol to show you all models. Most people forget this command and don't realize when additional models are available.

    32. Animations can be played in Protein Explorer, but not in RasMol.

    33. The rate of mutation in evolution can be displayed in colors using Protein Explorer's MSA3D, or even more easily with the new ConSurf Server. Patches of conserved residues, signalling functionally important regions of a protein, are easily identified.

    34. Installation: About the same small amount of fuss in each case.

    35. Off-line operation: Protein Explorer operates perfectly off-line (it can be downloaded, although you don't need to download it to use it from the web). RasMol's primary mode of operation is off-line, although a properly configured web browser can spawn it from some hyperlinks. Off-line use of either RasMol or Protein Explorer requires that the requisite PDB file(s) have been downloaded. When on-line, Protein Explorer can fetch a PDB file from any PDB mirror or other source, and get additional information from the PDB or other sources.

    36. Comparator mode allows two molecules to be compared side by side. Any operations of Protein Explorer can be directed at either or both molecules. RasMol has no such mode. (With either Protein Explorer or RasMol, you can run two sessions side by side. If each session is Protein Comparator, you can conveniently compare 4 molecules.)

    37. Protein Explorer comes with an extensive Help/Index/Glossary -- a "how to" guide that also defines some terms.

    Advanced Features

    1. You can load a PDB file by specifying its PDB identification code in the hyperlink to Protein Explorer, or within Protein Explorer in a form slot, or by browsing to a file on the local disk. RasMol can display from a hyperlink (as a helper application) or a local PDB file, but has no form slot for fetching a PDB code on-line.

    2. The ten most-recently loaded molecules (from local disk or Internet) can be reloaded from a menu in Protein Explorer. No such menu exists in RasMol.

    3. Protein Explorer has over ten preference options. The preference settings survive between sessions, and work regardless of whether Protein Explorer is used from the web, or a downloaded copy. There is an "expert" preference setting. RasMol has no preference settings, and is in "expert" mode all the time.

    4. In "expert" mode, when an NMR file is loaded, all models are shown in the initial view. A special NMR Model Selection page appears under Advanced Explorer, with the ability to play the ensemble of models as a movie, with custom-scripted rendering and coloring if desired. RasMol requires a special form of the "load" command in order to display more than the first model; most people forget this and don't realize when multiple models are available.

    5. In addition to the one-click menu selections (in QuickViews) that display cation-pi interactions or salt bridges, Advanced Explorer has detailed forms that offer additional control. These enable ligands to be included in the detection and display. This feature has its own tutorial.

    6. In addition to the one-click menu selection (in QuickViews) for displaying a solvent accessible surface, Advanced Explorer has a detailed form for configuring the display of multiple solvent accessible, rolling probe Surfaces**. Surfaces can be colored by molecular electrostatic potential or molecular lipophilicity potential**. Among many other options available in simple form slots, the probe radius can be changed.

    7. In addition to the one-click menu selection (in QuickViews) for showing a contact surface between any two moieties, Advanced Explorer has a detailed form for customizing the display of Contact Surfaces. This feature has its own tutorial.

    8. Advanced Explorer includes a Noncovalent Bond Finder that allows a very detailed exploration of the noncovalent bonds between any two moieties. This feature has its own tutorial.

    9. Protein Explorer has a command-line interface that understands nearly all* RasMol commands, plus additional Chime commands. In RasMol, going beyond looking at the entire molecule in various renderings and color schemes requires teletype-style commands. However, you don't need RasMol commands for effective exploration of macromolecules in Protein Explorer, since the menus are much more powerful.
        * "Nearly all": the "save" command is disabled in Chime, which precludes Protein Explorer from saving subsets of the atomic coordinates (but it can save the entire PDB file), exporting GIF's or vector postscript (but a screenshot saves a GIF from Protein Explorer), or saving scripts. (Protein Explorer copies the script to the clipboard, so it can be pasted into a word processor and saved.)

    10. Protein Explorer understands aliases for common commands, such as
      • s for "select"
      • spd for "set picking distance"
      • bs for "wireframe 0.15; spacefill 0.45 # ball and stick"
      • hb for "hbonds 0.2;color hbonds white;set hbonds sidechain;"
      • m for metals, by default "(cadmium,calcium,copper,iron,magnesium,manganese,zinc)"
      RasMol has no alias facility. In Protein Explorer, aliases are easily customized or added.

    11. Recent commands can be recalled and edited (to save retyping), a feature also offered by RasMol.

    12. Project folder. Both Protein Explorer and RasMol can work nicely from a project folder on the local hard disk containing PDB files and scripts.

    ** These features were built into Chime by the MDL staff that authored Chime (in some cases, at my request).