[phenixbb] R-factor problem !!!

hyang at rcsb.rutgers.edu hyang at rcsb.rutgers.edu
Sun Jul 29 12:35:57 PDT 2007

Regarding to the issue of easy PDB deposition, we do have a program called
pdb-extract which extracts the complete information from both the LOG file
and from the header of the pdb file generated by 35 crystallographic
programs/packages including Phenix.  So far, only the extracted TLS
information from Phenix can not be converted by ADIT during deposition. I
believe this will be resolved soon.

The web page of pdb_extract is http://pdb-extract.rcsb.org/
The new version

Please try the version 3.0 of pdb_extract and let me know for any
problems. Thanks.


> 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
> correction.
>> 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.
> Ralf
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