On Wed, Jan 25, 2012 at 1:29 AM, Tri Ngo
1. I'd like to run phenix refinement with twin data but I don't know how to define twin_law using GUI Phenix refinement module in Linux.
Open the Settings menu, look for "Twinning", and there should be a "Twin law" parameter in that dialog window. In the nightly builds I think I moved this to the main window, but I'll double-check.
2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high.
- I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448
- Then I use auto-weight to optimize the Rfree.
optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1
Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848
I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input.
I've found that weight optimization does tend to lead to lower RMSDs than I'd been taught to expect; I'm not sure why this is. They aren't necessarily wrong - but this may be indicative of some other issue. Do you have NCS? TLS would also be worth trying, since it sometimes helps with overfitting. -Nat