[phenixbb] R-factor problem !!!

Paul Adams PDAdams at lbl.gov
Mon Jul 30 10:13:31 PDT 2007

Hi John,

   you should probably download the latest prerelease of PHENIX (d7),  
from the web page. This contains a version of phenix.refine from  
early July.


On Jul 30, 2007, at 10:05 AM, john kryst wrote:

> Hi all !!!
>        Thanks a lot to all of you for your suggestions...  As many  
> of you have guessed it is a problem of Bulk solvent correction.  
> When i generated the pdb file using 0 cycles, the values are very  
> much comparable with phenix.refine. Interestingly CNS-1.2  
> xtal_pdbsubmission gave the same result as phenix.refine. which  
> once again confirms that its a bulk solvent correction problem.
> As Huanwang suggested, pdb_extract could generate submission ready  
> cif file.
> Once again thanks to all of you... But still i have problem with  
> rmsd_bonds. I am using phenix.refine version 2007_05_29_2026 .  
> Refmac gave rmsd_bonds 0.009 and rmsd_angles1.211 but phenix gave  
> rmsd_bonds 0.006 & rmsd_angles  0.793.
> 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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