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Hi Ajit-
Sounds like maybe you haven't defined the refinement to include your waters explicitly. Did you edit the parameter list near the top of the .ins file (like ISOR, CONN, BLOC commands) to include your newly added waters?

HTH-
Brad

On Fri, Feb 12, 2010 at 4:45 PM, Ajit Datta <[log in to unmask]> wrote:
Hello everyone,
  I have one more non-CCP4 related question again. I have been trying to refine a structure using SHELXL at ~1.0A. I added waters using SHELXWAT, however, it seems that the water molecules are not getting refined in the subsequent cycles. (B factor is at 50.00 for all of them). I can also see positive density at all the water positions with COOT.
  Can anyone let me know, what did I miss.

Thanks

Ajit B.