Rolf,
Are you looking for something more than
try{
} catch {
}
?
We've certainly had lots of experience running relatively complex scripts
on thousands of structures. We do it exactly as you describe -- with
JmolData and lots of structures.
Bob
On Fri, Oct 19, 2012 at 6:46 AM, Rolf Huehne <[email protected]> wrote:
> Dear all,
>
> I would like to use JmolData.jar for the analysis of several thousand
> PDB structures. Until now I used the strategy to start Jmol individually
> for each structure for automatic image generation for all PDB structures
> (or only new/updated structures). But this raises the processing time by
> a factor of 10 (or more) because starting Java and Jmol takes about 1
> second while loading a new structure took about 100 milliseconds on
> average within a test set of about 500 structures. For some structures
> Jmol needs only 5 to 10 milliseconds. So the gain might be even much
> larger, depending on the set of structures.
>
> Because Jmol scripting developed a lot since version 11.x (when I last
> developed something like this) I am wondering if it would now be
> possible to make a Jmol script error resistant (although I havn't found
> anything about this in the documentation or with Google)?
>
> In my case the idea would be to have a user-defined JmolScript function
> that would load a new structure and do some analysis. This function
> would be called for a list of structure files from a Jmol script. If an
> error would occur within the function (for example a load error) a
> specific customized error message would pe provided and the script would
> continue with the next structure.
>
> Regards,
> Rolf
>
>
> --
>
> Rolf Huehne
> Postdoc
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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