Hi Scott, you can do it in phenix.refine, please have a look at corresponding documentation page: http://phenix-online.org/documentation/refinement.htm#anch111 All you need to do is: 1) Place two chains into density (which I figure you've already done) 2) Make sure each chain has a non-blank altloc, say A and B 3) Run phenix.refine. If you need more help with this you can send me PDB file (and indicate chains in questions) and I will make sure it works correctly. Pavel On 5/2/14, 5:50 AM, Scott Horowitz wrote:

I have a strange case where I think there are two separate protein chains that are partially occupying the same spot (i.e. two proteins:one binding site=half of each bound). I'd really like to try to simultaneously refine both chains at partial occupancy into this density, but when I tried this (not surprisingly) it terminated because there were some overlapping atomic coordinates between the two chains. Is there a way to work around this?

Thanks, Scott