[phenixbb] R-factor problem !!!

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Sun Jul 29 10:13:12 PDT 2007

Hi John,

> 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 ??

Probably not. My guess is the difference is due to the bulk-solvent

> 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.

This is an ongoing project. We are doing some things differently
than other programs which requires discussions and adjustments
at both ends, PDB and us.

The phenix.refine PDB files contain almost everything the PDB needs
but they don't have the right tools to process this information.
Since phenix.refine is new there haven't been many submissions yet,
so the PDB hasn't had a big incentive to invest time (i.e. money)
to adjust the software at their end. Since it is difficult to
submit phenix.refine results, people run refmac or cns to prepare
for submission, which makes the PDB happy but doesn't solve the
problem. This is a bit of a chicken and egg problem.

Maybe if you also try refmac to see if the R-factors are better,
then submit whatever gives the best results, but also tell the
PDB that you'd much rather deposit the phenix.refine files directly,
you'd hopefully have a smooth deposition process but also make
the PDB understand that something needs to be done to help people
who used phenix.refine.


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