Re: [phenixbb] Problem avoiding real space refinement

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:

...

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

On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu wrote: performs global real-space refinement.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb