I guess it may not be a standard practice but I wonder if anyone has tried to use a density modified map for ligand building.

My situation is that I am trying to fit a single strand DNA ligand into an enzyme model. The dataset is at 3 Ang, P1 space, with overall completeness of only about 88%. MR was done by the apo-enzyme and the density for the first two-third of the ligand is very good and could easily be modelled. Towards the last one-third the density becomes much weaker so nucleotides cannot be easily put. This is the only dataset so far, so multi-crystal averaging / map averaging is not possible at this stage. NCS averaging is also not possible. We did try to sharpen map during refinement.

I understand that DM is usually used to improve phase at the initial stage esp. with experimental phasing. With MR would you think density modification could produce a better map to aid the modelling of the last one-third ligand? Can I use the denmod.mtz directly for manual model building?

Any input would be very much appreciated.

Best

Sam

Biochemistry Programme, CUHK