[ccp4bb] Composit omit map vs. ligand

[Petr Kolenko]

Dear colleagues,

we have a dataset with potential enzyme:ligand complex at 2.2 AA 
resolution. The ligand is very good substrate for the enzyme, we used 
soaking. We do not see the ligand in the regular difference electron 
density, only five out of twenty atoms. However, the ligand placed at 
the active site (model used from structure of a mutant variant) is 
refined well, giving no negative peaks in difference electron density 
map and nice observed electron density. I have calculated composit omit 
map with annealing in Phenix (input model did not contain the ligand) 
and the electron density for the ligand is there.

I have my own opinion, but we are desperate to obtain such data (more 
than 40 crystals already tested). My question is, would this be proof of 
presence of the ligand with reduced occupancy? Will this map convince 
the reviewers? Is there any other way to validate presence of the ligand?

Best regards,
Petr