If you put the coordinates into COOT it will give you a validation score.
If you use the CCP$i map correlation procedures it will also give you a
CC for the density match.
The input in each case is the reflection file with appropriate amplitude
and phase terms.
What you use depends on what phases are available.
Experimental phases - use FP PHI and FOM
Output of REFMAC refinement - maybe FWT and PHWT after you have excluded
the ligand from the refinement calculation?
Eleanor
Ask if you need more detailed ideas..
Qing Zhang wrote:
Hello,
I'm new in x-ray crystallography and trying to compute real-space
electron density for ligands. The goal is to evaluate match of ligands
with density peaks (like computing local R values in real space). What
would be the best electron density function that considers ligand
atomic numbers/radii, density map resolution, and some local protein
information (to estimate B values of ligand atoms)?
Thank you in advance.
Qing Zhang
