Caution: This is an Alpha version of Protein Explorer (PE).

This means that the newest features do not yet function perfectly, have bugs (known and likely unknown), and that documentation is in a preliminary state. Nevertheless, the new features are already beneficial, and some users will prefer having them. Please report bugs not on the known bug lists. If you prefer a more polished version, please use the Beta version at

The "Alpha" features are:

  1. PE's newest feature, MolSlides, saves annotated, rotating molecular views in small simple HTML files. MolSlides are ideal for research seminars, for teaching, and for reports by students. MolSlides can be played back as slides without PE, in Chime or Jmol. MolSlides can be imported back into PE to reorder, edit, merge sets, or apply the molecular view to PE (restoring the state of an earlier PE session). MolSlides can be converted to a PiPE, and (Windows only) inserted into PowerPoint slides (with spin/rotate and zoom). More & Examples..

    MolSlide development is supported only in Windows and only in Firefox, Netscape 7.2, or Mozilla. (Why?) Once developed, MolSlides can be viewed in a wide variety of platforms and browsers.

    To save your first MolSlide: Start a PE Session with any molecule. At any view, click Save This View.. (beneath the message box) and in the dialog that opens, click Add a MolSlide. The MolSlide Manager will then open automatically, containing help and directions. See also MolSlide Examples & FAQ.
    Go to PE Alpha!

  2. An Undo button. This is in the cluster of buttons that includes Spin, Zoom, Water. It can undo up to 25 previous actions (except for a few).

  3. The PE Recorder records most actions, and enables you to save and replay molecular views, and to go back to an earlier molecular view in your session History. (History is new in this release.) All controls for PE's Recorder are links located below the message box.

  4. Support for Presentations in Protein Explorer (PiPE). See examples and limitations. Presentations built now should work with future versions of PE with minor or no alterations. Access PiPE from the link to Presentations on the FrontDoor, or here.

Enter Protein Explorer Alpha

Summary of Recent Beta Versions
Complete, Detailed Version History

Reporting bugs: Tell us what computer platform you are using (Mac OS X, OS 9, or version of Windows), browser name and version, the PDB code loaded, and describe step by step (starting in a new PE session) the minimal process that repeatably shows the bug, not just the bad result. If the problem is in MolSlides, attach them to an email. If we can't replicate the bug, we can't fix it. Report to
MolSlides Known Limitations   --   Recorder Known Limitations   --   PiPE Known Limitations

MolSlides Known Limitations

  1. Export of MolSlides in Chime should work well. Although designed for a browser window 1024 x 768 pixels, they should display acceptably in a browser window 800 x 600 pixels or larger (see the viewing help at the bottom of the MolSlides).

  2. Export of MolSlides in Jmol is in a preliminary form. Molecular views exported to Jmol are not yet faithful to the originals in PE. The Export to Jmol presently has no options except for a window of 1024 x 768 pixels. Jmol MolSlides are presently fixed in size and will not adapt to larger or smaller windows.

  3. MolSlides can be converted to a PiPE, but this is a preliminary implementation. In particular, joined MolSlides are not supported yet in conversion to PiPE. Instructions for saving a MolSlide-PiPE have not yet been provided. (You simply display the PiPE header block from the link at the bottom of the PiPE control panel, copy it, and save it to a file as you would with a manually constructed PiPE header block.)

Recorder Known Limitations
Only bugs that affect function are listed. Problems with documentation are not listed, but feel free to report those too!

  1. For QuickViews DISPLAY Distances, Monitor Lines or Labels are not recording properly, and not undoable. If you perform these actions, you are warned before you proceed.

  2. In QuickViews, undoing a background color change leaves the help frame with the wrong (not matching) background color. Easy workaround: click the Bkg button twice. The same problem may occur when using Reset View...

PiPE: Known Bugs & Limitations
Only issues that affect function are listed. Problems with documentation are not listed, but feel free to report those too! See also the list of implemented capabilities in PiPE Specifications, and limitations removed/bugs fixed.

  1. A number of improvements in PiPE function have been achieved, and new example PiPEs have been linked. Also new, MolSlides can be converted to PiPEs. Creation of MolSlides requires no text editing and no knowledge of script commands, HTML, or javascript.

  2. Color keys can be constructed manually, but planned built-in convenience functions to show standard color keys, and a template for standard named colors, are not yet implemented.

  3. The Project Folder capability (for loading PDB files from the command input slot, and running .spt files) has been temporarily disabled. It remains available in PE 2.45 Beta.

  4. Reset View to FirstView does not work in a PiPE.

  5. When a button changes the PDB file, the Recorder is re-initialized. This means that the Undo and Save View operations do not extend back to earlier PDB files. Of course, pressing earlier buttons in the presentation can restore earlier views involving earlier PDB files.

Feedback to Eric Martz.