[phenixbb] explicit pdb output file name (refine)

Pavel Afonine PAfonine at lbl.gov
Wed Jan 20 22:21:14 PST 2010


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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>   
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