This is fixed for Jmol 11.7.6 and Jmol 11.6.2. For a revised set of Jmol
11.6 files, see http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
For an example of embedding PDB file data within HTML comments, see
http://chemapps.stolaf.edu/jmol/docs/examples-11/embed.htm
Bob
On Tue, Oct 28, 2008 at 12:29 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> 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
>
--
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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