doppelt olivia wrote:
I have a problem concerning the output_directory in modeller.I changed it on my script but the thing is that it generates errors because the restraint file and the .ini file is not found by the automodel script.Is there a way to only put the models in a file?? instead of modifying the entire output_directory??
You should avoid using output_directory, as it only controls the directory into which files are output, so (as you have discovered) it is worthless for any application which needs to read those files back in again. Modeller will produce its output files in the current directory by default, so simply 'cd' to the desired directory before running your script.
As I cannot see any application in which the output_directory variable would be useful, it will be removed from future releases of Modeller.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage