[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
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
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