Rolf,
I think what's happening is that the image is too complex. There is a
2-second timeout on the refreshing request, and that is done right before
the image is created. So in general, displays take less than 2 seconds, and
we have no problem. But if a display takes more than 2 seconds, Jmol ignores
the hold and continues -- this was important because in certain situations
Jmol would make a request to the operating system for a repaint, and it
would not be returned for some reason. I'm not saying I really understand
it. But that timeout on the rendering wait fixes that.
I believe it would work if you did this as a command line job with the -ion
flags set (silent, no console, no display).
With no display there won't be any rendering request. Please do try that.
Bob
On Wed, Apr 7, 2010 at 7:59 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote:
> On 04/07/2010 02:10 PM, Robert Hanson wrote:
> > Wow, thanks, Rolf. I thought perhaps you could do that! Oh, so close!
> >
> > First,
> >
> > write PNG
> >
> > just sends the image to your clipboard as an actual system-dependent
> image
> > since you didn't specify a file name. So it was trying to create that
> when
> > the error occurred. I'm guessing that happened not because the file was
> so
> > large but instead because the ribbon was so tiny. I'll see if I can
> > reproduce that.
> >
> I repeated it with a filename (I thought without one the application
> would ask for one in a file select box, but I remember now that a
> question mark is needed for that) and now only got the following error
> message:
>
> java.lang.ArrayIndexOutOfBoundsException
> rendering error?
>
> The image was written but it looks distorted:
> http://www.fli-leibniz.de/ImgLibPDB/tmp/1m4x-biol_unit-full-distorted.png
>
> It should look like this one (generated with C-alpha only):
> http://www.fli-leibniz.de/ImgLibPDB/thumbnail/manual/1m4x.pdb1_small.gif
>
> Regards,
> Rolf
>
>
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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
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