Hi Ralf,

in fact, phenix.refine outputs information about refined f' and f'' in ready-to-PDB-deposit format under RAMARK 3 prefix. For eample:

REMARK   3 
REMARK   3  ANOMALOUS SCATTERER GROUPS DETAILS.
REMARK   3   NUMBER OF ANOMALOUS SCATTERER GROUPS : 2    
REMARK   3   ANOMALOUS SCATTERER GROUP : 1    
REMARK   3    SELECTION: name BR
REMARK   3    fp  : -0.8792       
REMARK   3    fdp : 5.8029        
REMARK   3   ANOMALOUS SCATTERER GROUP : 2    
REMARK   3    SELECTION: name CO
REMARK   3    fp  : 0.0000        
REMARK   3    fdp : 0.0000        
REMARK   3


I hope this information is preserved when such structures get deposited into PDB -:)

Pavel.


On 1/20/10 9:44 PM, Ralf W. Grosse-Kunstleve wrote: 
Do I understand correctly that there is no way to force refine to skip
the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb?
    

Yes, that's true.
The main reason is that the same run writes
  foo_001.eff
  foo_002.def
When I implemented this I thought the serial numbers are the only
practical way to keep things straight.
Later we added storage of refined f' and f" to the .def file (since
there is no place in the .pdb file that would survive passes through
external programs). Because of this the serial numbers seem even more
important to me.
Ralf
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