On Tue, Nov 5, 2013 at 7:46 AM, Ryan Spencer 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. -Nat

Thank you guys for the suggestions. I changed the occupancy of the ligand to 1 in pdb and do refinement with 'refine occupancies' box checked. The R values dropped about 3-4% compared with before and the occupancy for the ligand stays as 1. Thank you! Best, Wei On Tue, Nov 5, 2013 at 11:17 AM, Ryan Spencer wrote:

That is true although I think even when I changed the HETATM tag to ATOM and went through Phaser it still changed the unknown ligands back to HETATM and dropped the occupancy to 0.00. I could be wrong on this. Either way it’s not a big issue to edit the PDB directly or even in Coot under edit>residue info and set everything back to 1.00 before starting refinement.

Ryan

*From:* [email protected] [mailto: [email protected]] *On Behalf Of *Nathaniel Echols *Sent:* Tuesday, November 05, 2013 7:55 AM

*To:* PHENIX user mailing list *Subject:* Re: [phenixbb] Green density for ligands in places where the ligand is in density

On Tue, Nov 5, 2013 at 7:46 AM, Ryan Spencer 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.

-Nat

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