[phenixbb] Fitting ligand with DM map?

Sam Tang samtys0910 at gmail.com
Sat Jun 3 11:33:24 PDT 2017

Dear community

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

Any input would be very much appreciated.


Biochemistry Programme, CUHK
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