[phenixbb] Green density for ligands in places where the ligand is in density

Nathaniel Echols nechols at lbl.gov
Tue Nov 5 07:54:43 PST 2013

On Tue, Nov 5, 2013 at 7:46 AM, Ryan Spencer <rspencer at uci.edu> wrote:

>                 The pdb of the ligand probably had an occupancy of 0.00
> when you brought it into Coot. The easiest way to handle it is to just
> change all the occupancies of the ligand back to 1.00 in the pdb. If the
> ligand has partial occupancy then phenix might be dropping it down to 0.00
> if you have the ‘refine occupancies’ box checked. I’ve seen this before
> when doing MR with ligands that phenix does not recognize without the
> corresponding .cif.

That actually has nothing to do with the CIF - by default Phaser will set
the occupancy to zero for anything labeled as a heteroatom (i.e. HETATM
lines in a PDB file), which the exception of some non-standard or modified
amino acids such as MSE.  It's not clear if that's what's happening in
Wei's case; I'm pretty sure eLBOW doesn't normally output ligands with an
occupancy of zero.

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