[phenixbb] Problem avoiding real space refinement
Pavel Afonine
pafonine at lbl.gov
Thu Oct 27 10:12:16 PDT 2011
Hi,
yes, this is exactly it. Sorry, I keep promising to clean this
naming/conception mess one day. Hopefully (thanks Herb), this day is
approaching fast!
Pavel
On 10/27/11 8:51 AM, Nathaniel Echols wrote:
> 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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