[phenixbb] refine occupancies for MET/MSE double conformations

Anastassis Perrakis a.perrakis at nki.nl
Tue Nov 4 03:46:11 PST 2008

Hi there  -

I was pleased to read in the manual:

if no selections are provided (refine.occupancies.individual=None and  
refine.occupancies.group=None) then phenix.refine by default will  
refine individual occupancies for atoms that have partial occupancy  
values in input PDB file (except zeros) and it will perform group  
constrained occupancy refinement for all atoms in alternative  
conformations. Occupancies of all other atoms will be fixed.
If selections are provided  
(refine.occupancies.individual=atom_selection or  
refine.occupancies.group=atom_selection) then the selected atoms will  
be added to the list of atoms defined above (atoms with partial  
occupancies or those in alternative conformations). See this document  
for examples of atom_selection syntax.

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  
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.adp.tls="chain A"
refinement.refine.adp.tls="chain B"
refinement.refine.adp.individual.anisotropic =" chain C"
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,

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