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. Cheers, Paul 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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