It is possible to save the animation window to a local HTML file. You can then bookmark the saved file, and play back the animation window in Netscape or Internet Explorer without running Protein Explorer. Examples of saved HTML files can be found in PE's Atlas of Macromolecules under Enzymes.

There are some minor limitations to this method. The only controls that will work in the saved animation window are the Animate toggle button, and the Close link. The Scripts link won't display the scripts (though they can be seen with View Source).

Here is the procedure:

1. It is strongly recommended that you first save the PDB file to your disk. This is especially important if you wish to run the saved animation off-line. (The tutorial has a section How do I download a molecule?) Then run Bare PE, and use the Browse button to load the saved PDB file.

2. The [Bkg] (background color) button won't work in the saved animation window. Therefore, use the [Bkg] button on the NMR Models/Animation page to establish the desired background before starting the animation that you will save.

3. The Zoom, Stereo and Center buttons won't work in the saved animation. Therefore be sure to orient and zoom the molecule as desired before pressing the [Animate] button. The orientation and zoom will automatically be established in the animation window (by the automatic insertion of a "view set" command). If you want the animation to have a center of rotation other than the center of the entire molecule, or to be in stereo, you will need to customize the script in the box on the NMR Models/Animation page before starting the animation that you will save. This can be done by inserting these commands immediately before the line "#--End color scheme--":
   select [atoms to be centered]
   center selected
   stereo 5

   The command "stereo 5" is for divergent stereo; use "-5" for convergent.

   Substitute appropriate atom expression where indicated by brackets. Do not include the brackets "[ ]" in your commands. To find how to phrase the "atoms to be centered", either copy a select command generated by using the SELECT menu in QuickViews, or click on a single atom to get its serial number, and use the command "select atomno=[serial number]", or consult Select Commands in Chime and RasMol.

4. Scroll to the bottom of the NMR Models/Animation document (usually the upper left frame) and check the checkbox Optimize animation window for saving to a disk file.

5. Type a suitable title for your animation in the slot below the checkbox.

6. Press the [Animate] button to create the animation window. Try the [Animate] button in the new window and verify that the animation works, and that the orientation, zoom, and background color are as you wish. (If not, repeat the previous steps making appropriate adjustments.)

7. Save the animation window to an HTML file on your disk:
   • Netscape: In the animation window (after toggling the animation off), open Netscape's File menu and select Save As. Give the file a suitable name ending in ".html".
   • Internet Explorer (IE): In the animation window, open IE's View menu (at the top of the window) and select Source. A Notepad window will open displaying HTML code. In the Notepad window, open the File menu and select Save As. Give the file a suitable name ending in ".html".

8. Close the animation window after saving the HTML file. This is necessary because if it remains open while you open the saved file in another Netscape window, the animation toggle button may affect the wrong window (crosstalk).

9. Open a new browser window, and use File, Open Page, Choose File (IE: File, Open, Browse) to open your saved animation file.

10. Bookmark, Add! Later, you can use the bookmark to display the saved animation file.

11. You will need to press the [Animate] button to start the animation.

12. For maximum portability (such as putting your saved animation on a server, or moving it to a different computer):
    1. Place the saved HTML file together with the required PDB file in the same folder.
    2. Open the HTML file in Wordpad or Notepad in Windows, or BBEdit on the Mac. Do not use Word or an HTML editor as it may ruin the HTML file.
    3. Use the Edit, Find function to locate file:/// (include the colon!).
    4. Remove the absolute path from in front of the PDB filename. For example, if you find

       src="file:///N:/erics1ws/chime_pe/current/shared/1lcd.pdb"

       change it to

       src="1lcd.pdb"

       This makes the HTML file look in its own folder for the PDB file.
    5. Save the modified HTML file, being sure to save it as a plain text (.txt) file (same as DOS text or ASCII text). Do not save it as a .doc file!

13. Examples of saved HTML files can be found in PE's Atlas of Macromolecules under Enzymes.