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I haven't had the good fortune of using SHELXL in a few years, but I seem to recall that you need to make sure that you don't have an END statement preceding your newly added waters.  Check this after each cycle of SHELXWAT.

best wishes
kmj

On Fri, Feb 12, 2010 at 1:45 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.