Please Note: When MolSlides are exported to Jmol by this version of Protein Explorer, the molecular views may not always be faithful to the originals in Protein Explorer. We expect to correct this in future releases of Protein Explorer. If the renderings in Jmol are not satisfactory, please export your MolSlides to Chime. Also, please email to us your MolSlides to help us find and fix these issues.
A 1024 x 768 pixel window in a browser with current java is required for correct display of the MolSlides below.   Viewing Help, Downloading, & Troubleshooting.. (at bottom).
Spacebar/Enter for next slide, Backspace for previous.   More keystrokes.. (at bottom)
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Introduction to MolSlides by Eric Martz, University of Massachusetts, Amherst MA USA MolSlides.ProteinExplorer.Org Eric Martz is the main author of Protein Explorer, which includes the MolSlides development software. Made with MolSlides.ProteinExplorer.Org

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MolSlides display views of molecular structures that you generate from ProteinExplorer.Org. Saving a MolSlide takes only a few mouse clicks. MolSlides display in a web browser, without Protein Explorer, from your computer or from a server, on-line.

MolSlides can be displayed in Chime or Jmol. Chime supports a limited set of browsers (Windows and Mac Classic only), while Jmol supports more, including Safari (Mac OSX), Mozilla in linux, and more. (Details). Made with MolSlides.ProteinExplorer.Org

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Because MolSlides are easy to make, students can use them for reports, as well as faculty for tutorials, and researchers for seminars. Shown: Salt Bridges.

The hardest part of making MolSlides is learning how to use Protein Explorer (PE). But PE is easy to use. Molecular views are modified with buttons and menus, with levels for beginners through experts. Extensive help is built in, starting with Flash movies that demonstrate how to use PE. Learning the Chime/RasMol command language is unnecessary. Made with MolSlides.ProteinExplorer.Org

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Two molecular views can be compared in one MolSlide. You control whether molecules spin at the outset, or not. Dragging the molecule with the mouse always rotates it.

The background can be black or white. Secondary structure: Alpha Helix, Beta Strands. Made with MolSlides.ProteinExplorer.Org

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The bottom view follows the top view when you drag (or zoom) the top with the mouse. (Following works only with Chime in Windows, not on Mac Classic nor with Jmol.)

Secondary structure: Alpha Helix, Beta Strands. Amino to Carboxy termini, with a rainbow sequence in between. Zoom: hold down Shift while dragging up or down. Made with MolSlides.ProteinExplorer.Org

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The MolSlide Manager Built into Protein Explorer, the MolSlide Manager makes it easy to add text to your molecular images, reorganize your slides, import and merge sets, join and separate comparison slides, or copy all or portions of MolSlides. You can preview the slides, then save them permanently at any time. Made with MolSlides.ProteinExplorer.Org

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Animations of molecular conformational changes can be saved from Protein Explorer. These can be linked to MolSlides. Shown here: Specific Binding of the Lac Repressor to DNA Bends the Operon Double Helix. If the image in this slide is not animated, press Reload. The image in this slide is an animated GIF, not a rotatable/zoomable view. Click the "Specific Binding ..." link above to see the animation interactively in Chime. Here is the full story on the Lac Repressor animation. More about Animations in Protein Explorer. Made with MolSlides.ProteinExplorer.Org

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Save/Restore Protein Explorer's State Any molecular view in a MolSlide can be applied to Protein Explorer, producing the same image, and allowing you to begin further exploration from the view saved in the MolSlide. Made with MolSlides.ProteinExplorer.Org

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Invitation to Download, Import, Adapt You are welcome to download this set of MolSlides for a class website, or any use in accord with the copyright statement. Instructions for downloading are below. You are also welcome to import this set of MolSlides into Protein Explorer (ProteinExplorer.Org) and incorporate selected slides, or modifications thereof, into new sets, provided the original author is credited with the copyright statement intact. If you are not viewing this set of MolSlides from ProteinExplorer.Org, visit MolSlides.ProteinExplorer.Org to see if it has been updated. This copy was last updated June 15, 2006. The End Made with MolSlides.ProteinExplorer.Org

• Here are the recommended browsers.
• Maximize your window, then View, Full Screen (F11).
• For a small (800 x 600 pixel) window, reduce the text size (View, Text Size). Then Reload the MolSlides.
• Keystroke controls (not all work in every browser, but the links above each slide Next, Previous, 1, 2, ... 9 always work.):
  • Next Slide: Spacebar, Enter, Down Arrow, Right Arrow, PgDn.
  • Previous Slide: Backspace, Up Arrow, Left Arrow, PgUp.
  • Slide Number: 1-9.
  • First Slide: Home, Esc.
  • Last Slide: End.

• Please respect the copyright statement, if any is present in these MolSlides.
• Make a new folder (directory) to receive your MolSlides.
• Save the MolSlides themselves with your browser's File, Save As. (Some browsers may not save the MolSlides correctly. On Windows, these browsers are known to work well: Firefox, Netscape 7.2, Mozilla.)
• Save each PDB file needed by this set of MolSlides (see list below under Troubleshooting). Click on the Jmol frank at the lower right corner of each molecular view, and choose the top item on the menu, a 4-character "PDB ID code". On the submenu, choose the bottom item, a code plus ".pdb". If a black browser window opens showing a wireframe rendering of the molecule (in MDL Chime), click on the MDL frank at the lower right corner and choose File, Save Molecule As.
• You will also need the files JmolApplet.jar, JmolApplet0.jar, ... JmolApplet6.jar available from Jmol Download.
• Double-click on the MolSlides HTML file to view it, or drag and drop it onto or into the browser you wish to use.

Can't see the molecule(s)?
• This set of MolSlides uses the Jmol java applet, which requires Java on your computer. Some Windows computers need java (free) installed from java.com. (Also, the folder/directory supplying this MolSlides file must contain the JmolApplet#.jar files.)
• If some (or all) slides have blank rectangles without any molecules, some (or all) of the necessary PDB files may be missing from the folder (directory) supplying this MolSlides file. This set of MolSlides needs the following PDB files:
    1d66.pdb, 1pgb.pdb