I am new to phenix. I am tring to refine the occupancies using the phenix.refine gui. In the refinement settings- refinement strategy : occupancies , when I define the groups for individual atoms as chain A and resseq 1:200 (for protein atoms) and a ligand group in constrained as chain B and resseq 1:10 and chain C and resseq 1:10, the refinement fails with several errors. The refinement runs fine when I do not touch the "occupancies" panel on the gui.

Actually, right now the GUI doesn't handle all of the options for occupancy groups - they were too complicated to generate the interface automatically. I'll see if I can fix this. What are the errors you get, and could you please describe your structure in more detail? Based on the above, I don't think you want to refine occupancies for chain A - you only need to do this for atoms that have alternate conformations or that really aren't 100% present (e.g. ions, also some larger ligands). Is the ligand group in two conformations or do you really have two different chains?

How do I refine in Phenix the occupancies defining as well as partitioning the molecule as individual, groups and coupled groups?

Right now you'll need to do this on the command line, but if you can wait a day or two I may have this part of the GUI fixed. In version 1.4-3 and above, the parameters are this: refinement.refine.occupancies { individual = None remove_selection = None constrained_group { selection = None } } All of these may occur multiple times. The documentation says: individual: Selection(s) for individual atoms. None is default which is to refine the individual occupancies for atoms in alternative conformations or for atoms with partial occupancies only. remove_selection = Occupancies of selected atoms will not be refined (even though they might satisfy the default criteria for occupancy refinement). constrained_group = Selections to define constrained occupancies. If only one selection is provided then one occupancy factor per selected atoms will be refined and it will be constrained between predefined max and min values. Constrained groups are only required when you have two different sets of atoms (e.g. different chains, or different residues in a single chain, or a ligand/water and a protein chain, etc.) whose alternate conformations are coupled. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]