Zheng Zhou wrote:
Hi, All
Could any tell me how CCP4 handle free R flag? I know It is important
to select the same** FreeR reflections if I move to next step of
refinement. But everytime I start from fresh, the freeR Flag remains
unchanged. The Rwork and Rfree of my models are fine ( 20.7% and
22.9%). I thought Rfree was randomly generated. I asked more
experienced people in the lab and neighbor labs, and didn't get a
straight answer. Did I do something wrong?
Thanks and sorry to bother others.
Zheng (Joe)
You have two options for setting the FreeR flag in CCP4i. You can do it
at the time of scaling in SCALA by ticking the button "Ensure unique
data & add FreeR column for x.xx fraction of data." 5% of the data is
the default, which may be excessive depending on the number of total
reflections you have.
If you did not set the FreeR flag during scaling, you can do it later
using the Convert to MTZ & Standardise task under Reflection Utilities
in the GUI. Tick "Create a full unique set of reflections and generate
FreeR data" and select your FreeR fraction in the box near the bottom of
the task window.
Once the FreeR flag is set it should not change, and you should not
generate a new set of FreeR flags again during the refinement. The idea
is to set aside some data early on that is never used to refine the
model so that it is as unbiased as possible in evaluating your
refinement statistics and guarding against model bias. When refining
with Refmac5, tick the "Exclude data with freeR label FreeR_flag with
value of 0" to ignore the FreeR data during refinement.
Cheers,
--
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Roger S. Rowlett
Professor
Colgate University Presidential Scholar
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