OK, I can reproduce it. It's definitely a bug. No need to send any files.
On Tue, Oct 28, 2008 at 12:04 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> 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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>
>
>
> --
> 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
>
--
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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