![](https://secure.gravatar.com/avatar/27ba568f99cd0f771e5ef0d4784716f8.jpg?s=120&d=mm&r=g)
- Could you give some tips about refinement at this resolution other than rigid body refinement - Can TLS and grouped B-factors work at this poor resolution ?
I did the refinement of a low resolution (4.1 A) structure of a 20S proteasome where I used one TLS group per domain or per ring, and one B-factor per domain. I used R-free set selected in shells because of the high degree of NCS but didn't get a significantly higher R-free than selecting at random (did not study this at great length). Actually I think this structure was the reason I first started using phenix.refine, because AFAIK this is the only program that can do this combination (TLS and grouped B). Context: 20S has 14 copies each of 'A' and 'B' subunits (segids AA* and BB* respectively). Something like this (edited to spare you all 28 segids): refine { strategy = *individual_sites rigid_body individual_adp *group_adp *tls adp { group = "segid AAA1" group = "segid AAA2" group = "segid AAA3" group = "segid AAB1" group = "segid AAB2" etc one_adp_group_per_residue = False tls = "segid AAA*" tls = "segid AAB*" tls = "segid BBA*" tls = "segid BBB*" } ncs { find_automatically = False restraint_group { reference = "segid AAA1" selection = "segid AAA2" selection = "segid AAA3" selection = "segid AAA4" selection = "segid AAA5" selection = "segid AAA6" selection = "segid AAA7" selection = "segid AAB2" etc coordinate_sigma = 0.07 b_factor_weight = 10 } restraint_group { reference = "segid BBA1" selection = "segid BBA2" selection = "segid BBA3" selection = "segid BBA4" selection = "segid BBA5" selection = "segid BBA6" selection = "segid BBA7" selection = "segid BBB2" etc coordinate_sigma = 0.07 b_factor_weight = 10 } } } Not exactly the best structure I've ever done, but 14-fold averaging was useful. In the above case I was doing TLS on entire A7 or B7 rings (segid AAA* = segids AAA1-7) rather than per-domain TLS. PDB code 3H4P REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.325
- I would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I
Why particularly trust the molecular replacement solution with an imperfect model ? If you are just doing rigid body refinement, I'd argue that the rigid body results *define* the NCS at least for that model. NCS restraints would have no effect on the results of rigid body (if the boundary definitions were consistent). Phil Jeffrey Princeton