When you are using the unsigned applet locally, all files loaded must come
from the directory containing the JAR file or a subdirectory of that. So you
are doing:
....\mydir\jmol\JmolApplet0.jar
....\mydir\cccccc.pdb
That's not allowed on a local machine.
I recommend using the signed applet. Change:
jmolInitialize("jmol");
to
jmolInitialize("jmol", true);
On Sat, May 22, 2010 at 5:30 AM, Maurice Schroff <[email protected]>wrote:
> 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_Inhibitor
>
> -Eric
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> 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
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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