[phenixbb] R-factor difference between phenix and sftools

[Tim Gruene]

Dear Simon,

I found this a very puzzling observation and given the high throughput
of this board, it is likewise puzzling you have not received a reply yet
- or have you?

Best regards,
Tim

On 10/12/2014 08:25 PM, Simon Jenni wrote:
> Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors
> are:
> 
>    Final R-work = 0.3221, R-free = 0.3638
> 
> phenix.cc_star agrees:
> 
>    phenix.cc_star com_001.pdb com_001.mtz \
>    f_obs_labels="F-obs,SIGF-obs" \
>    f_model_labels="F-model,PHIF-model" \
>    unmerged_data="xscale.hkl"
> 
>    r_work: 0.322
>    r_free: 0.364
> 
> so does phenix.model_vs_data:
> 
>    phenix.model_vs_data com_001.pdb com_001.mtz
> 
>    r_work          : 0.3221
>    r_free          : 0.3638
>    sigma_cutoff    : None
> 
> However, when I calculate the R-factors with sftools, I get a discrepancy
> between the phenix and sftools results:
> 
>    sftools << eof
>    read com_001_f_model.mtz
>    Y
>    select col R_FREE_FLAGS > 0
>    correl col FOBS FMODEL
>    select invert
>    correl col FOBS FMODEL
>    quit
>    Y
>    eof
> 
>    R-work: 33.6
>    R-free: 38.1
> 
> Does anyone perhaps know what causes this difference?
> 
> With best regards, Simon
> 
> PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS
> (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497).
> No indication for a P21 twin (L-test and refinement in P21 with twin law),
> not higher symmetry spacegroup I222 (alternating strong and weak
> reflections are visible in the diffraction patterns, resolved structural
> differences in the two protomers of the dimer). Two datasets from different
> beamlines. As might be expected, the R-factors after refinement are
> unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36
> with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between
> different programs to see how they cope with the unexpected bimodal
> amplitude distribution.
> 
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 173 bytes
Desc: OpenPGP digital signature
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20141013/b476dec3/attachment.sig>