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