This error occurs both with Windows and Linus versions of Modeller 8v0 when 'a.final_malign3d = True' is left in the script file. If this statement is commented out and the script is otherwise unchanged, it works just fine. The job gets stopped right at the very end, presumably before the models are fitted to the template.
Similar thing happens when these two lines are in the script:
mdl = model(env) mdl.optimize(optimization_method=3, max_iterations=50, output='REPORT', trace_output=1)
In this case, however, the script dies at the beginning. Again, commenting out these two statements is all it takes to get the job going. I'll send the error messages to Ben only, the whole list probably doesn't need to see them.
Any suggestion/advice is appreciated. Cheers,
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: firstname.lastname@example.org | ==========================================================================
Mensur Dlakic wrote: > This error occurs both with Windows and Linus versions of Modeller 8v0 > when 'a.final_malign3d = True' is left in the script file. If this > statement is commented out and the script is otherwise unchanged, it > works just fine. The job gets stopped right at the very end, presumably > before the models are fitted to the template.
Could you send me your input files and the .log file for this, please? I can't reproduce your problem here. Does the automodel/model-fast.py example crash on your systems (it works here) ? That example uses final_malign3d.
My guess is that malign3d is unable to fit your models for some reason, but it shouldn't crash with a segmentation fault (as your followup to me indicated) - it should give an error message, so that you can figure out how to fix your script!
> Similar thing happens when these two lines are in the script: > > mdl = model(env) > mdl.optimize(optimization_method=3, max_iterations=50, > output='REPORT', trace_output=1)
I'm not sure what you're trying to do here. Assuming that 'env' is a previously created 'environ' object, this will try to optimize a model containing no atoms and no restraints. That won't work at all. On my system Modeller does give an error message in this case (although it crashes immediately afterwards, which will be fixed).
Ben Webb, Modeller Caretaker