Hi there  -


I was pleased to read in the manual:


However, I want to refine my MET residues in double conformations, one as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy to start with. When I try that I get:

==
        ----------Initial model statistics (before refinement)----------       
...
|-Occupancies statistics------------------------------------------------------|
Sorry: There are atoms with negative occupancies. Check input PDB file.

===

The PDB file has 0.5 and 1.0 occupancies only.

I am also using:

==

refinement.refine.strategy=tls+individual_sites+individual_adp+group_anomalous
refinement.refine.adp.tls="chain A"
refinement.refine.adp.tls="chain B"
refinement.main.number_of_macro_cycles=4
refinement.simulated_annealing.start_temperature=5000
refinement.refine.adp.individual.anisotropic =" chain C"
refinement.input.xray_data.labels=I_Mystery(+),SIGI_Mystery(+),I_Mystery(-),SIGI_Mystery(-),merged
refinement.refine.anomalous_scatterers {
  group {
    selection = "name ZN "
    f_prime = -0.3
    f_double_prime = 2.5
    refine = *f_prime *f_double_prime
  }
  group {
    selection = "name SE "
    f_prime = -5.2
    f_double_prime = 3.8 
    refine = *f_prime *f_double_prime
  }
}

==


Any hints on how to proceed ? Should I define groups for the occupancy refinement explicitely and not rely to automatic assignment?
And if so how? How do people treat this partial Se-Met issue ? We solved the structure with SeSAD ...  if I out MSE I get pretty large negative density peaks on the Se ... if I put MET I get positive peaks ;-) And there are good reasons to believe in partial Se-substitution in this case.

Thanks in advance,

Tassos