Saving the Animation Window
from the NMR Models/Animation page.
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 without running Protein Explorer. Although Protein Explorer
will not run in Internet Explorer, the saved animation HTML file
will. (The animation is jumpier in IE, but it works.)
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:
- 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.
- 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.
- 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.
- Press the [Animate] button to create the animation window. 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".
- 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).
- In any Netscape window, use File, Open Page, and then the Browse
button, to open your saved animation file.
- Bookmark, Add! Later, you can use the bookmark to display
the saved animation file.
- You will need to press the [Animate] button to start the animation.