The true structure is shown in brown, the MR model in green.
Model bias leads to density around the MR coordinates.
An electron density map can be calculated using the phases from the model obtained by molecular replacement. Ideally this will show regions of the model which are in error - either missing or misplaced atoms. A cross-validated, sigma-A weighted map is calculated using the CNS task file model_map.inp:
cns_solve < model_map.inp > model_map.out [1 minute]
Overall the map is good, but there are some regions in which the density is poor. This is because there are differences between the search model and the true structure and also differences between the two molecules in the asymmetric unit. In particular the N-terminal residues in the two monomers adopt very different conformations. The poor density in this region in molecule B suggests that these residues may initially need to be omitted from refinement.
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| Sigma-A weighted map (at 1.5 sigma) calculated using the MR model. The true structure is shown in brown, the MR model in green. Model bias leads to density around the MR coordinates. |