- a87_99_h.pdb is derived from 1us0.pdb by:
- extracting 87-99 residues from chain A;
- removing alternative conformations and setting occupancies to 1;
- adding H atoms;
- placing model into a P1 box: iotbx.pdb.box_around_molecule;
- setting B-factors to 80.
- converting all residues to GLY.
This model is the reference ("answer"). It contains information about helix H-bonding that is defined from actual expetimenatl diffraction data.
- Compute simulated diffraction data:
phenix.fmodel a87_99_h.pdb add_random_error_to_amplitudes_percent=5 type=real high_res=4 low_res=6 r_free=0.1
mv a87_99_h.pdb.mtz data.mtz
Given that we introduce 5% error into Fobs, we expect the best possible R-factor after refinement to be ~5%.
-
run_perturb.py generates many perturbed models - starting points for refinements.
-
Run Q|R refinement, sample command:
python ../qr-core/qrefine.py a87_99_h.pdb.mtz perturbed/1.5/4.pdb restraints=cctbx update_all_scales=False
- run_analyze.py is to analyze the results.
example analyze.dat
| Pert. Dose | Min dist. | Max dist | Av. dist. | % recovered |
|---|---|---|---|---|
| 0.3 | 1.880 | 2.734 | 2.239 | 45.56 |
- 2mFo-DFc calculated map, comamnd:
phenix.maps data.mtz a87_99_h.pdb