[phenixbb] Problem avoiding real space refinement
Nathaniel Echols
nechols at lbl.gov
Thu Oct 27 08:51:28 PDT 2011
On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu <JNwachuk at scripps.edu> wrote:
> We noticed that in some of our refinements, real space refinement was
> performed even though we chose not to do this.
> I tried to opt out of real space refinement as follows:
> " refine {
> strategy = *individual_sites individual_sites_real_space rigid_body \
> *individual_adp group_adp *tls *occupancies group_anomalous
> ..."
> however, the R-free is identical whether we select real space refinement or
> not, and the logfile shows
> " Validate:
> |--------START--------| |--------FINAL--------|
> residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc
> "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00
> "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<<
> "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43
> "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00
> "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<<
> "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<<
> "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90
> ... "
> and suggesting that real space refinement was performed.
That's the rotamer fitting - technically, it's an independent step
(fix_rotamers=True) The individual_sites_real_space strategy only
performs global real-space refinement.
-Nat
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