[phenixbb] WAS: changing TLS groups mid refinement
pjeffrey at princeton.edu
Tue May 18 08:12:42 PDT 2010
No. You've missed the point here.
Pavel Afonine wrote:
> Dear Phil,
> on a further thought about your "Longer version":
>> Default behavior yields:
>> Final: r_work = 0.1898 r_free = 0.2479 bonds = 0.007 angles = 1.114
>> Truncate=yes data yields:
>> Final: r_work = 0.1932 r_free = 0.2473 bonds = 0.007 angles = 1.113
> these Rfree-factor results above seem "identical" to me (we can compare
> them since they were the same for both refinements).
Except they are absolutely not the same set of reflections.
phenix.refine throws away the weakest data in the "default behavior"
case. It throws away 5.7% of them. There are fewer reflections (read
down the email and look at the Remark 3's from the PDB file).
Truncate includes this data in the truncate=yes case, which contains
more reflections (see Remark 3), this additional data will be weaker, so
you'd expect R-free and R-work to be higher.
I even agree that it's not wise to compare these two R-free's, which is
why I created the data subset in the last test in my earlier email.
A more ideal test would be to remove the extra truncate=yes reflections
from the test set. However I don't know of any program that will do
that (at least not with my current mtz file) and I'm not going to hand
edit the data since I'm actually using this data. Regenerating a test
set would involve concerns about removing work set bias from the new
test set, and that's a can of worms I do not want to enter into.
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