Right, it is just standard minimization as described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h...> "It is intended for cleaning up small molecule structures and improving localized interactions within larger systems. It may not be able to resolve large-scale distortions or widespread structural problems. By definition, energy-minimization simply moves the system toward a local minimimum without crossing energy barriers, and does not search for the global minimum." On Jan 15, 2013, at 9:31 AM, Bobo Dang wrote:
Got it, I submitted a bug report with the pdb file I am working on.
One more thing, the minimize function in Chimera is just to give a minimized structure in the local environment, it does not cross the energy barrier to give the structure which has the minimum energy of the system, is that right?
thank you
bobo