[Jmol-users] Re: Jmol novice question

[Miguel <mi...@jm...>]

> I have used RasMol and Chime for several years, and just downloaded Jmo=
l
> yesterday.  A have a few naive questions I wonder if you could help me
> with.

Joel,

You should join the jmol-users=40lists.sourceforge.net mailing list.

Do not be afraid to post even *simple* questions ...

> 1) =22Where is it?=22  I know it's a browser plug in, but it doesn't sh=
ow up
> in my IE plugins folder or my Mozilla Firefox plugin folder.

The Jmol Applet is an applet, not a plugin. It must live on the web
server. It automatically gets downloaded when a user visits the web page.=


For example, when someone visits www.jmol.org the Jmol Applet
automatically gets downloaded/executed on their machine. The only browser=

requirement is that Java be installed.

As an end-user, you do not need to explicitly download the Jmol Applet
unless you are setting up a web site.

> 2) I hear it's a stand alone program, but can it be opened like RasMol

Yes, the Jmol application is a stand-alone Java program that can be run
from the command-line ... or an icon can be set up to launch it.

> (&
> if so, from where - there's no icon and there's no jmol.* on searching =
for
> files),

There is currently no nice/fancy installation of the Jmol application.

It is a Java application and the application is named Jmol.jar ... locate=
d
in the root of the file that you downloaded/unzipped.

For running on Windows there is a jmol.bat file there.
For running on MacOSX/Linux/Unix there is a shell file named jmol

On Windows:
c:=5C> cd =5CJmol
c:=5CJmol=5C> jmol samples=5Cxyz=5Ccaffeine.xyz

On MacOSX/Linux/Unix
=24 cd /path/to/jmol
=24 ./jmol samples/xyz/caffeine.xyz

If you want an icon, then post a question to the mailing list and someone=

will tell you how to do it ... I don't know how.

> or only used =22invisibly=22 with a browser, as with Chime.
Nope

> 3) After I downloaded Jmol, when I used Mozilla Firefox to go to a Chim=
e
> Tutorial I've used before, the Chime images were missing and replaced b=
y a
> message to download the plug in.

This had nothing to do with Jmol.
Jmol does not replace Chime on the client.
Rather, the person who set up the web site needs to modify their web site=

to serve/send/use the JmolApplet.

> Clicking on the icon, =22no plugins were
> found.=22  (IE works).  I went to MDL.com and downloaded Chime (again) =
but
> Chime still doesn't show up as a Firefox plugin, nor does Jmol.

Correct

> I would appreciate any help to get me to square one.  Thanks.

You can use the Jmol application as an alternative to RasMol

You should use the JmolApplet directly *only* in the case where you are
setting up a web site.

As a casual end-user of Jmol, you do not need to do anything ... the
JmolApplet will get automagically downloaded when you visit a web site
that has been prepared with Jmol.



Miguel

-----
Open Source Molecular Visualization
www.jmol.org
miguel=40jmol.org
-----