[phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

Heather Condurso condurso at bc.edu
Thu May 30 07:09:32 PDT 2013

Samuel, Nat, and all,

I have a similar issue.  My data is nearly perfectly twinned so Xtriage usually fails to find any twin law.  However when I solve the structure in the lower symmetry space group with twinning my maps look beautiful.  In the higher symmetry space group, only 3 of the 6 monomers fit into nice looking density.  I simply use generate table 1 and uncheck the box so it won't regenerate R factors.  The discrepancy between the R-factors is however much more significant than 2%.  From refine I get 18/22 and from table1 28/31.   


 |  On Wed, 29 May 2013 17:18:57 -0700
 |  Nathaniel Echols <nechols at lbl.gov> wrote:
 |  On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer <Samuel.Stampfer at tufts.edu> wrote:
 |  > When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in
 |  > the documentation that twinning can account for some of this discrepancy,
 |  > but that the program is supposed to take twinning into account if it will
 |  > lower the calculated R-work by more than 2%, which it doesn't seem to have
 |  > done (or there is some other problem with my data).
 |  Okay, the problem is that your data don't actually appear to be
 |  twinned.  The automatic method used by phenix.model_vs_data (which is
 |  used internally for Table 1 and the validation GUI) only tries
 |  possible twin laws if the results of the "L test" show a suspicious
 |  distribution of intensities.  Your data look fine, so it doesn't
 |  bother trying the twin laws.  That the R-factors are lower when you
 |  refine with a twin law isn't necessarily indicative of the data
 |  actually being twinned - Garib Murshudov has looked into this in
 |  detail but I confess to being ignorant of the math (but I can probably
 |  dig up his paper on the subject if anyone is interested).  However,
 |  I'm pretty sure the data are actually in a higher-symmetry space
 |  group.  Will send details and new files off-list (probably tomorrow at
 |  this rate).
 |  I should probably change some of the programs and/or documentation to
 |  make it more clear what is being done internally, since it took me a
 |  bit of digging to realize what was going on.  In general, though,
 |  always be very careful before running twinned refinement!  I have seen
 |  several users do this by mistake when they really had higher symmetry.
 |   The maps will also be more model-biased when using twinned
 |  refinement, so it's good to avoid doing this unless absolutely
 |  necessary.
 |  -Nat
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