Hi Yarrow, ok, I wish that error message (that I put a while ago, in 2009 to be precise) lists those atoms... Can you send me the file so I can tell you what these atoms are? In general, if at rigid-body refinement stage you have atoms at special positions it is unlikely to be right. Pavel On 6/17/14, 12:56 PM, Yarrow Madrona wrote:

Hi,

I am trying to do rigid body refinement, however I get an error in phenix telling me that there are atoms at special positions.

I am not sure how to determine which atoms are at special positions so that I can exclude them from rigid body refinement. Can someone help me with this? Thank you.

-Yarrow