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Copyright 2006 by Eric Martz,
University of Massachusetts, Amherst MA USA.

Permission is hereby granted to use this document, or portions thereof, for non-profit educational purposes, provided this copyright statement remains intact within this document, or any portions or derivatives. Other uses require explicit permission from the author.

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.
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Introduction to MolSlides

by Eric Martz, University of Massachusetts, Amherst MA USA


Eric Martz is the main author of Protein Explorer, which includes the MolSlides development software.
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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).
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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.
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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.

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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.
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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.

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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.
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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.

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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.
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