Hi Dana, Unfortunately there is no way to minimize and treat some part as a (moving) rigid body. You can only specify that some atoms should not move at all, with the"spec" and/or "freeze" options. The frozen atoms will still exert forces on the others unless you also use the "fragment" option to ignore them completely. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 13, 2013, at 11:51 PM, danashah@post.tau.ac.il wrote:
Hi all, We're interesting in performing a structure minimization for a model, while treating a part of the model as a rigid body. Is "fragment true" the best way to do that, or is there a different option?
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html#fragment
Of course the "spec" option will define all the atoms which are not in the rigid body part.... Best, Dana.