It appears that in my IExplorer, right clicking and going to the molecule
name does nothing. However, in Firefox, it does open up a new window with just
the molecule. And I am allowed to Save As... I have Chime installed in both.
In a message dated 10/30/2005 1:31:03 P.M. Eastern Standard Time,
> Is there way to save from a Jmol presentation.
The answer is ... probably yes, but it depends upon your browser
In most prerelease versions of Jmol the top item in the popup menu is the
name of the file (or name of the molecule). That popup brings up a menu
with atom counts. The last item on that menu is the name of the file.
Select that file and the browser will probably put up a dialog box asking
you what to do with the file. You can then save the file.
It is a simple question, but the answer is somewhat complicated.
Unsigned applets have security constraints in order to protect people from
viruses. Therefore, unsigned applets (including Jmol) cannot write to (or
read from) the local hard disk.
So, Jmol itself cannot directly save the molecule to your hard drive.
However, an applet is able to ask the web browser to open up a window to a
new URL. Therefore, Jmol can construct a URL to the molecular model file
and ask the browser to open that file as a URL. How that is treated will
depend upon the configuration settings of both the web server and the web
* The web server will look at the file name extension and send back a
MIME type based upon that extension.
* The web browser will use that MIME type to figure out what to do with
* If the web browser has not been configured with any plug-ins (like
Chime) OR if the file was compressed with .gz compression then the
browser will not have a special handler for that MIME type and the
browser will bring up a dialog box, asking the user what to do with the
file. The user can save the file to the hard disk. Note that it is the
browser and the user who are saving the file to the hard disk, not the
* If the web browser was previously configured with the Chime plugin,
then the browser will probably recognize the MIME type and will bring up
a new browser page with Chime.
* Internet Explorer has some special handling and does not always follow
the rules for MIME types. For example, it might recognize the fact that a
.xyz (or .mol, or .pdb) file looks like a text file and it might choose
to display the text file in the browser itself. One can then save the
file from the browser.
* If one has control over their web server AND they are not running the
Chime plugin against the same web server, then one could configure the
chemical MIME types on the server so that the server always tells the
browser to pop the dialog box. This would (should) guarantee that the
end-user is always prompted with a dialog box and is given the
opportunity to save the file.
Sorry ... it is ugly ... but that is the way it is.
If anyone has any ideas on how to simplify this process I am open to
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