On Feb 7, 2012, at 11:13 AM, Elaine Meng wrote:
This approach requires using the minimize command and its "fragment" option, only available in the command (not GUI), and in fairly recent builds of Chimera 1.6.
In fact there is a bug in AddCharge in the most recent build that will trip you up with the 1a6m structure. The bug is fixed now and will be in the next successful build.