[phenixbb] Problem avoiding real space refinement

Jerome Nwachukwu JNwachuk at scripps.edu
Thu Oct 27 10:42:32 PDT 2011


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 Biology
Scripps-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<JNwachuk at scripps.edu<mailto: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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