Please send me a copy of an HTML file that is causing this problem with the
embedded PDB file.
Also, there is another option for loading a file inline. You can simply have
your server include the PDB data in the form of an HTML comment, then create
a bit of JavaScript that extracts that out of the HTML (using
document.body.innerHTML and a bit of splitting, for example) and sends it to
Jmol using the jmolLoadInline() function. This has the advantage that no
line formatting is necessary.
But it still should work.
Bob
On Tue, Oct 28, 2008 at 4:06 AM, Chris Pudney
<[EMAIL PROTECTED]>wrote:
> G'day,
>
> I'm upgrading our site's installation of JmolApplet from v10.0.0.42 to
> v11.6.1 (we want to render Mopac data).
>
> In the main there have been no problems. However, when it comes to PDB
> data containing multiple models Jmol v11.6 displays the error message:
>
> "No atoms found for file string type pdb"
>
> I don't use the JavaScript library to generate the Jmol applet tag,
> preferring to have the server to render the applet tag directly. Thus,
> the applet tag looks something like,
>
> <object
> classid="java:JmolApplet"
> codetype="application/x-java-applet;version=1.4.2"
> height="600"
> width="800">
> <param name="cache_archive" value="JmolApplet.jar">
> <param name="cache_version" value="11.6.1.0">
> <param name="codebase" value="http://solstice-v1.rt.intra:8000/java";>
> <param name="codebase_lookup" value="false">
> <param name="image" value="">
> <param name="loadInline" value="Multiple model PDB data with |
> used as line-separator"
> <param name="script" value="model all">
> </object>
>
> This worked fine under Jmol v10. Additionally, single-model PDB data
> loads fine with v11.6.
>
> I've tried removing the "script" parameter but get the same result.
>
> Searching for the "no atoms found" error message lead me to this posting:
>
> http://www.mail-archive.com/[email protected]/msg09043.html
>
> but the problem there is caused by Jaguar files and the | character.
>
> Any suggestions on how to use the loadInline and script parameters to
> render multi-model PDB data with v11.6 would be greatly appreciated.
>
> Thanks,
> Chris.
>
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--
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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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