Interesting. I've also noticed that lines (such as those shown below) are missing from the logfiles whether I select *individual_sites_real_space or not.
|-LOCKIT real space refinement (target=simple): start-------------------------|| r_work=0.2098 r_free=0.2283 rmsd bonds=0.004 angles= 1.03 ||-----------------------------------------------------------------------------|
|-LOCKIT real space refinement (target=simple): end---------------------------|| r_work=0.2203 r_free=0.2521 rmsd bonds=0.004 angles= 0.74 ||-----------------------------------------------------------------------------|
Could it be that the global *individual_sites_real_space strategy was actually not performed in either case? I would be glad to send you the logfiles off list, if that would be more helpful.Thank you,
-Jerome
Jerome C. Nwachukwu, PhD
Nettles' Lab
Dept. of Cancer BiologyScripps-FL
x3297
On Oct 27, 2011, at 1:12 PM, Pavel Afonine wrote:
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<[email protected]> 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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