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Dear Kavya What about using occupancy refinement in refmac? link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy refinement. R On 12 Apr 2013, at 17:12, Kavyashree Manjunath <[log in to unmask]> wrote: > Dear users, > > Is it advisable to refine the occupancy of > a ligand for a 2.0Ang data by approximately > changing the values of occupancy based on > its b-factor? > After refinement, there were some negative > densities appearing in some parts of the > ligand, like at the centre of a pyrimidine > ring, so I expected that the problem is with > the occupancy. (the crystal was obtained by > co-crystallisation method). > Kindly provide some suggestions. > > Thanking you > With Regards > Kavya > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > Roberto A. Steiner Group Leader Randall Division of Cell and Molecular Biophysics King's College London [log in to unmask] Room 3.10A New Hunt's House Guy's Campus SE1 1UL London Phone 0044 20 78488216 Fax 0044 20 78486435