Hi
In a recent structure we have recently obtained by x-ray diffraction and solved by MR, we actually see obviously positive density for which we are quite confident to account for our ligand. However when we model the ligand in (with full occupancy), negative density appears.
So in this case should I adjust occupancy to a lower value, or let the refinement programme to adjust the B-factor?
Hi Sam
Fitting of the ligand in the electron density map should be done in the last cycles of your refinement. What I mean here is, once you get the MR solution, make sure you do as many cycles of model building and refinement of your macromolecule until the R factors converge. This will improve the overall electron density map and the density for the ligand will be more clear. When you first model the ligand in the map, by default the occupancy will be 1.0. In the subsequent refinement cycles, include the cif file of your ligand and allow the program to refine both the occupancy and B-factors for all atoms. I hope this helps. Best wishes.
I mostly agree with Avinash. Be careful that you select a plausible occupancy model of your ligand. Some programs let you refine per-atom occupancies, but a single occupancy for your entire ligand is much better. If you have a good theoretical reason to assume your ligand is cleaved, you may need two use two occupancies for your ligand.
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