[phenixbb] problem with high Rfree

Peter Zwart PHZwart at lbl.gov
Mon May 19 14:26:13 PDT 2008

Hi Christopher,

The free set is made with the symmetry of the lattice in mind.
For instance, when you have a dataset with unit cell dimensions
20 20 20 90 90 90
and assigned spacegroup P1, it will take into account ALL possible
twin laws in assigning the free set.



2008/5/19, Rife, Christopher L <crife at slac.stanford.edu>:
> And on a related note, how can one be sure that the FreeR set that phenix.refine is generating takes the given twinning operator into account? From the log file output, it seems like the FreeR set is generated before it gets to any of the twin statements.
>  I have the following in my file, and I can see during the refinement that it is indeed doing twin refinement, however I want to ensure that it's using a reasonable FreeR set.
>   twinning {
>     twin_law = "-h,-k,l"
>     detwin {
>       map_types {
>         aniso_correct = True
>       }
>     }
>   }
>   r_free_flags {
>     fraction = 0.05
>     max_free = 5000
>   }
>  Thanks!
>  Chris
>  ________________________________
>         From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Christina Bourne
>         Sent: Monday, May 19, 2008 1:32 PM
>         To: phenixbb at phenix-online.org
>         Subject: [phenixbb] problem with high Rfree
>         Hello BB,
>         I am working on a structure that is twinned (merohedral) in P41.  Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far).  My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol.  I have data from 48-2.8A.
>         I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension.  During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK.  (Yes, I am trying to grow different forms)
>         Maps look nice, although I wish my ligand had more/better density.
>         I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true.  My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270.  Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530).  I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong.
>         Why is my Rfree hanging so high?  Is it becaues I have bad karma?  Is it to do with the twinning?  I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43).  There isn't room for anything else in the cell.
>         Any opinions or suggestions are most welcome as I wait for better xtals to grow...
>         Thanks in advance,
>         Christina
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:     http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
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