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Hi, I am refining a structure at 1.7 Ang structure in Refmac. I see peanut-shaped positive electron density which have been suggested to be alternate positions of water molecules. I modelled these positions as water molecules with the same residue number, but labelled as different conformers, with partial occupany. Refmac run with arp_waters, renumbers the alternate positions as 2 separate water molecules with 2 different residue numbers. The map calculated after this step, shows the positive density as being not satisfied too. ATOM 2839 OW0AHOH W 22 -13.265 25.298 20.692 0.50 15.94 O ATOM 2840 OW0BHOH W 22 -13.494 26.740 21.658 0.50 26.75 O after Refmac becomes, ATOM 2839 OW0AHOH W 22 -13.265 25.298 20.692 0.50 15.94 O ATOM 2840 OW0BHOH W 23 -13.494 26.740 21.658 0.50 26.75 O The same happens when I tell arp_waters to merge atoms that are less than 1 Ang apart. If I run Refmac with no arp_waters, one of the alternate positions is discarded, leaving behind the line for other conformaer with 0.5 occupancy. How do I overcome Refmac's renumbering of the alternate water positions? Thanks, Preethi.
