[phenixbb] R-factor problem !!!

Paul Adams PDAdams at lbl.gov
Sun Jul 29 10:14:44 PDT 2007

Hi John,

   we are working on a deposition header for the PDB files. The R-factor 
differences you see between phenix.refine and CNS are probably because 
of differences in the bulk solvent model (or TLS if you used it). The 
differences in the bond rmsd is a result of a bug in the reporting of 
these numbers in phenix.refine. If you obtain the latest version (d7) of 
the phenix prerelease this problem should be fixed.


john kryst wrote:
> Hi all !!
>       I am using phenix.refine to refine my 3.2 A structure. Also i use 
> xtal_pdbsubmission utility in CNS to generate pdb file which is 
> submission ready format. Please note no refinement in CNS only formating.
> Phenix.refine gave a R and Rfree of  0.1929 &  0.2512 ( rmsd bonds = 
> 0.006 )  respectively. When i format in CNS it gave R and Rfree 0.2282 & 
> 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ??
> As for as i know we cant generate a  submission ready PDB format from 
> phenix.refine. Is it possible to implement it, which will be very 
> helpful for all of us.
> Thanks in advance for your inputs
> regards
> John
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Paul Adams
Senior Staff Scientist, Physical Biosciences Division
Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909

Lawrence Berkeley Laboratory
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Berkeley, CA 94720, USA.

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