On 04/23/2010 07:50 AM, Armin Meier wrote:
When comparing the printed phi/psi angles, I expected the very first ones (i.e. the first ones printed into the log-file, right at the start of optimization) to be the same as the phi/psi angles extracted from the *.ini file, because this is the starting point. But this isnt at all what I see.
It sounds like you are running automodel, in which case the .ini file is the starting point, but before the first step of optimization, the coordinates are randomly displaced (otherwise each optimization would simply give you the same results). If you want to be sure your energy function is working, you'd be better off to generate a few test restraints on a static structure and then just call selection.energy() to test it.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage