Hi Everybody, First off, thanks for the replies. They definitely fixed my problem. It was indeed as Garib Murshudov said. The flags got swapped, and therefore the percentage of Rfree reflections were 95%.
So, if Rfree is created from CCP4.....use Rfree flags with a value of 0 and a value of 1 if the Rfree was created with PHENIX. Both maps now look the same, and it indeed looks like the protein in the crystal is different from the sequence. Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
