Hi, <br>I want to use phenix to refine a model right after autobuild with the following script:<br>phenix.refine xray_data.file_name=exptl_<div id=":3b" class="ii gt">fobs_phases_freeR_flags.mtz overall_best-090903a.pdb strategy=rigid_body+individual_sites simulated_annealing=true simulated_annealing.start_temperature=8000 sites.rigid_body="chain A" sites.rigid_body="chain B"<br>
<br>However, the program says "<br>F-obs:<br> exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP<br><br>If previously used R-free flags are available run this command again<br>with the name of the file containing the original flags as an<br>
additional input. If the structure was never refined before, or if the<br>original R-free flags are unrecoverable, run this command again with<br>the additional definition:<br><br>refinement.input.xray_data.r_free_flags.generate=True<br>
<br><br>when I use phenix.mtz.dump exptl_fobs_phases_freeR_flags.mtz, it indicates that it has FreeR_flag=1. Can anyone tell me why there is FreeR_flag in my data, while the refinement program does not recognize it?<br> label #valid %valid min max type<br>
H 35619 100.00% 0.00 22.00 H: index h,k,l<br> K 35619 100.00% 0.00 45.00 H: index h,k,l<br> L 35619 100.00% -33.00 33.00 H: index h,k,l<br> FP 35619 100.00% 0.00 114.22 F: amplitude<br>
SIGFP 35619 100.00% 0.15 6.13 Q: standard deviation<br> PHIM 35619 100.00% 0.00 0.00 P: phase angle in degrees<br> FOMM 35619 100.00% 0.00 0.00 W: weight (of some sort)<br> FreeR_flag 35619 100.00% 0.00 1.00 I: integer<br>
FC 35619 100.00% 0.00 0.00 F: amplitude</div><br>