Is there a way to explicitly control which atoms end up in pkfrag1 and pkfrag2?  Specifically, I'd like to be able to move/rotate fragments which are made of multiple molecules or are internal loops.  Using pkbond or pkatom to break between fragments doesn't give me enough control.  Selecting and protecting atoms doesn't seem to help, in this case.
Dave Horita
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email:  dhorita@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/