From: Robert H. <ha...@st...> - 2010-04-07 13:12:53
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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 <rh...@fl...> 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 > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 |