Dear Dr. Henson,
as I get the e-mails of the Jmol mailing list I thought of asking a probably
very easy question for you to answer. As I am currently working on a
presentation on Jmol for my Abitur (Germany), I would like to create a
Jmol-webpage. To try this out I copied the source code of
http://jmol.sourceforge.net/demo/atoms/.
Altered to my website it is:
<html>
<head>
<title>jmol applet atoms demo</title>
<script src="jmol/Jmol.js"></script>
</head>
<body>
<script>
jmolInitialize("jmol");
jmolCheckBrowser("popup", "../../browsercheck", "onClick");
</script>
<table border="1">
<tr>
<td>
<h2>cyclohexan</h2>
<script>
jmolApplet(400, "load cccccc.pdb");
</script>
</td>
<td>
<form>
<p>
The RasMol scripting language has two synonymous
commands to control atom size, <b>spacefill</b> and
<b>cpk</b>
(for Corey, Pauling, and Koltun). The commands are
aliases and run
exactly the same code.
</p>
<script>
jmolRadio("spacefill on",
"spacefill on <i>or</i> cpk on <i>or</i> spacefill
100%<br />");
jmolRadio("spacefill off",
"spacefill off <i>or</i> cpk off <i>or</i> spacefill 0
<i>or</i> spacefill 0%");
</script>
<p>
As an extension to the RasMol scripting language, Jmol
allows you to specify your size as a percentage of the
vanderWaals radius.
</p>
<script>
jmolRadio("spacefill 20%", "spacefill 20% <i>or</i>
cpk 20%<br />", "checked");
jmolRadio("spacefill 25%", "spacefill 25% <i>or</i>
cpk 25%<br />");
jmolRadio("spacefill 50%", "spacefill 50% <i>or</i>
cpk 50%<br />");
jmolRadio("spacefill 75%", "spacefill 75% <i>or</i>
cpk 75%<br />");
</script>
<p>
If you want to specify a fixed size then you can do so
in Angstroms.
Note that the last button specifies "1.0" instead of
the integer "1".
This is important because integer values specify
<i>RasMol units (1/250th Angstrom)</i>
</p>
<script>
jmolRadio("spacefill 0.25", "spacefill 0.25 <i>or</i>
cpk 0.25<br />");
jmolRadio("spacefill 0.5", "spacefill 0.5 <i>or</i>
cpk 0.5<br />");
jmolRadio("spacefill 0.75", "spacefill 0.75 <i>or</i>
cpk 0.75<br />");
jmolRadio("spacefill 1.0", "spacefill 1.0 <i>or</i>
cpk 1.0<br />");
</script>
</form>
</td>
</tr>
</table>
</body>
</html>
Nearly everything works except the Jmol applet. Jmol loads but then there is
an output of an error message
"java.security.AccessControlException:accessdenied (java.io File Permission
C:\Users..."
I read that this problem could be solved by adding the lines
grant {
permission java.security.AllPermission;
};
To the java.policy file, however it did not work for me, do have an advice
what I could to ?
I am looking forward to hearing from you
Sincerely,
Maurice Schroff
Von: Robert Hanson [mailto:[email protected]]
Gesendet: Freitag, 21. Mai 2010 19:42
An: [email protected]
Betreff: Re: [Jmol-users] Uses for MDL Sculpt
Fun. It makes a nice point that molecules are flexible.
Probably still a notch above what we are talking about here -- so far, the
minimization is restricted to the molecule containing the atom pulled, and
all other atoms are ignored.
Bob
On Fri, May 21, 2010 at 12:20 PM, Eric Martz <[email protected]>
wrote:
At 5/21/10, Philip Bays wrote:
>Yes, both the Sculpt and the smiles conversion applet are fixed. Thanks.
>
>I tend to agree with Angel and Rich on the Sculpt
>capability. While it is really cute, I am not sure how to use
>it. I played with Sculpt when it first came out years ago. Could
>never figure out what to use it for then either:-(
Here's the most fun thing I ever did with MDL Sculpt (Mark Surles'
program), now shown in Jmol.
(Its a simulation of an HIV protease inhibitor binding to the
protease with sidechains adjusting)
N.B. click on the "Play Animation" button in the section "Molecular
Playground Animation" to see the simulation. The sidechains appear
near the end of the animation.
http://proteopedia.org/wiki/index.php/Molecular_Playground/HIV_Protease_Inhi
bitor
-Eric
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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