Hi Jeff, phenix.refine default behavior of occupancy refinement is described in great details here: http://www.phenix-online.org/version_docs/1.9-1690/reference/refinement.html... It describes command line scenario but it fully applicable to the GUI as well. If you do not wan to refine ligand occupancy just set it to 1 for all atoms. If you want to refine partial occupancy for the ligand (one occupancy for all atoms, NOT individual occupancy for each atom), just set occupancy to some number less than 1 to all atoms in the ligand. Then phenix.refine will recognize what you want autocratically , no need to set any parameters. Please let me know if you have any questions or need any help with this. Pavel On 5/7/14, 6:21 AM, Kieft, Jeffrey wrote:

Hello All,

Question about occupancy refinement. I'm refining an RNA structure at 2.0 Angstrom resolution with bound ligands iridium hexammine and spermine. The location of the former can be confirmed in an anomalous difference map, but they are likely not full occupancy...likewise the spermine is likely less than one. When I use occupancy refinement, it leaves the RNA at full occupancy as expected, but refines each atom of the irhex and spermine individually, in some cases driving the occupancy to 0 for some atoms.

It seems like this was an issue in the past, but I'm still seeing it. Any ideas? Could if be that Phenix doesn't recognize those ligands? Parameter files wrong?

Thanks for help!

Jeff

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