MolSlides.ProteinExplorer.Org
Introduction and FAQ
(Frequently Asked Questions) for
Rotating 3D Macromolecular Structure Slides
Created with ProteinExplorer.Org
  1. See Examples of MolSlides in Chime and Jmol
  2. My MolSlides (available here after you download PE and create some)
  3. What are MolSlides?


  4. Jmol or Chime can be used to display MolSlides, once they are made.
  5. Which browsers are best for viewing MolSlides?

  6. Making MolSlides requires Windows with Firefox, Netscape 7, or Mozilla.
  7. Making MolSlides requires free MDL Chime.     Test Your Chime Here!
  8. How do I make MolSlides?

  9. Where should I save my MolSlides?
  10. How do I import MolSlides into a PE session?
  11. How do I restore a PE session from a MolSlide?

  12. How do I make small changes to the molecular view in an existing MolSlide?
  13. How do I show more than one molecule (PDB file) in a single set of MolSlides?
  14. What are the keystrokes that control a MolSlide show?
Making MolSlides requires free MDL Chime:
How do I make MolSlides?
  1. Although many browsers and platforms work well for viewing MolSlides, for creating them, only Windows, and only Netscape 7.2, Firefox, or Mozilla are supported. If you happen to use a different browser, a red notice will appear automatically.
  2. Go to ProteinExplorer.Org and find PE version 2.76 or later.
  3. Start PE, displaying a molecule of interest.
  4. Achieve a molecular view that you might like to show in a MolSlide.
  5. Click Save This View.. (below PE's message box), and in the dialog window that opens, click Add a new MolSlide.
  6. The MolSlide Manager will open automatically showing your molecular view. The MolSlide Manager has extensive built-in help that displays automatically. Once it is open, you will see how to proceed.
  7. Make sure you Export to Save and then save the MolSlides HTML file to disk (in your MolSlides Folder) before you close your PE session!
Where should I save my MolSlides?

The answer depends on whether you are working from a downloaded vs. an on-line copy of Protein Explorer (PE). Look in the browser's address slot near the top of this window. If the address begins http, PE is on-line; if it begins file, this is a downloaded copy.

From downloaded PE: The standard location for your MolSlide Folder (Directory) is:   my_molecules\molslides\myslides
If you have downloaded a copy of PE, the parent folder my_molecules\molslides will have been created for you. If you have not already done so, you will need to create the folder myslides in my_molecules\molslides. Then, save your MolSlides files into myslides. All PDB files needed by your MolSlides must be saved into the same folder as the MolSlides files themselves. Save the PDB files from the MolSlide Manager -- this ensures that the PDB filenames will match those in your MolSlides. (How to save a PDB file.)

From on-line PE: If you have not downloaded PE, you can save MolSlides anywhere, preferably into a new empty folder, or a folder that already contains MolSlides you saved earlier. All PDB files needed by your MolSlides must be saved into the same folder as the MolSlides files themselves. Save the PDB files from the MolSlide Manager -- this ensures that the PDB filenames will match those in your MolSlides. (How to save a PDB file.)

If you later download PE, you can move MolSlides files you saved from on-line PE sessions to my_molecules\molslides\myslides at that time, if you wish.

A Single Folder is OK for Multiple Sets of MolSlides: You may have as many different MolSlides folders as you wish (each containing its own PDB files). However, there is nothing wrong with putting different MolSlide sets (each in its own HTML file) in the same folder. If these sets use some PDB files in common, this will avoid needing multiple copies of the same PDB files in different folders. Don't Save Files into the PE Folders! Never save any of your own files (PDB, MolSlides, etc.) in the Protein Explorer folder or its subfolders (shared and protexpl) because these will be replaced whenever you upgrade to a new version of PE. Files or folders you create in my_molecules will not be touched, although certain files there bundled with PE may be upgraded along with PE.

When starting a new MolSlide development session, after you have previously saved MolSlides, load the PDB file from your MolSlides Folder: At PE's FrontDoor, start Empty Explorer. After PE starts, you will see the Load Molecule control panel. Use the Browse button to load the PDB file from your MolSlides Folder. This is especially important when your set of MolSlides uses more than one PDB file. Loading the PDB file from your MolSlides Folder tells PE where to find all the PDB files so all molecular views in the set will display properly.

To check where the PDB file came from in the current PE session, click Session Info.. below the message box).
How do I import MolSlides into a PE session?

You may import MolSlides that you have saved, or MolSlides created by others, into PE. (Please respect the copyrights of others! Ask for permission if your planned use is not explicitly permitted in the copyright statement.)
    Importing MolSlides from your computer's disk:
  1. This procedure applies to MolSlides you have saved from a previous PE session, or downloaded to your computer's disk. (If you wish to import MolSlides from an on-line URL, go to the next section.)
  2. Start PE by opening Empty Explorer (available at PE's FrontDoor).
  3. "Empty" PE will start at the Load Molecule control panel. Use the Browse button to load a PDB file (molecule) from the folder (directory) containing the MolSlides you wish to import. If there is more than one PDB file there, choose one that is used in a molecular view in the set of MolSlides you plan to import.
  4. Click on Import Views.. (beneath the message box), and follow the instructions there.
  5. After you have imported a set of MolSlides, PE's MolSlide Manager will open automatically, displaying the imported slides.

    Importing MolSlides from an on-line URL (single PDB file):
  6. Look at the bottom of the MolSlide set for the list of PDB files, under Troubleshooting, to see whether the set uses more than one PDB file. If the set uses only one PDB file, this procedure will work. If there is more than one PDB file involved, go to the next procedure.
  7. Start a new PE session, loading the PDB file needed by the MolSlides you wish to import. You can simply specify a PDB identification code in the slot at PE's FrontDoor, or load a PDB file from your local disk (by starting Empty Explorer from PE's FrontDoor). (If the PDB file is not a published one, and you don't have a copy of it, use the procedure below for multiple PDB files.)
  8. Click on Import Views.. (beneath the message box), and follow the instructions there.
  9. After you have imported a set of MolSlides, PE's MolSlide Manager will open automatically, displaying the imported slides.

    Importing MolSlides from an on-line URL (multiple PDB files):
  10. Look at the bottom of the MolSlide set for the list of PDB files, under Troubleshooting, to see whether the set uses more than one PDB file. If the set uses two or more PDB files, this procedure will work. This procedure will also work when there is only one PDB file involved, but you don't know how to start a PE session to display that file.
  11. Download the set of MolSlides to your computer's disk. The procedure for downloading is at the bottom of the MolSlides, after the last slide.
  12. Verify that you can view the MolSlides from your downloaded copy. If there is a problem, see Troubleshooting at the bottom of the MolSlides themselves.
  13. Now, go to the procedure above for importing MolSlides from your computer's disk.
Once you have imported MolSlides, you may Apply one to PE (thereby restoring the session for the molecular view saved in the MolSlide). You may also reorder the imported MolSlides, edit their text, or change the molecular views, and then save the revised set. By importing two or more sets of MolSlides, you can merge sets, reorder them, and delete slides you don't want.
How do I restore a PE session from a MolSlide?

The molecular view in each MolSlide represents the state of a previous PE session. You can restore that state from the MolSlide. Once restored, you can continue to explore the molecule from the restored view, possibly saving additional MolSlides as you go.
  1. Import the set of MolSlides containing the molecular view that you wish to restore (see these instructions).

  2. Click Apply to PE next to the molecular view that you wish to restore.
You can apply any molecular view to PE, at any time, from the set of MolSlides in the current session of PE.
How do I make small changes to the molecular view in an existing MolSlide?

The general idea is that you Apply your existing molecular view to PE, use PE to change it, then Add the revised molecular view as a new MolSlide, then Copy the revised molecular view into the old slide. Here it is in more detail:
  1. Start PE, loading the molecule that is in the MolSlide you wish to change.
  2. If the MolSlide you wish to change is not already in your PE Session, import it (using the link Import View.. beneath PE's message box).
  3. Open the MolSlide Manager (using the link beneath PE's message box).
  4. Click on Apply to PE above the molecular view you wish to change.
  5. Use PE to change the molecular view.
  6. Add the revised molecular view as a new MolSlide (using the link Save This View.. beneath PE's message box).
  7. In the MolSlide Manager, touch the Copy link above the revised molecular view. In the help at right, select the option Copy molecular view only.
  8. Click Copy and specify the number of the MolSlide you wish to revise as the target of the copy. This replaces the old molecular view with the revised one, keeping the remainder of the slide intact.
  9. Optionally, use the Delete link above the temporary copy of the now superfluous, revised molecular view at the end of your slideset.
How do I show more than one molecule (PDB file) in a single set of MolSlides?



See also Where should I save my MolSlides?.
What are the keystrokes that control a MolSlide show?

Keystrokes are usually the most convenient way to move through your slides. If these keystrokes do nothing, click with the mouse on any text in the document, to focus the document. If keystrokes still don't work (likely with Mac OSX and non-Safari browsers) use the Next and Previous links.

In addition to the keystrokes, there are links for Next, Previous, and slide numbers that allow you to jump directly to any slide number. These links always work, while keystrokes don't work in some browsers.

Feedback to Eric Martz.