low resolution refinement question
Dear Phenix users, I refine a large complex with three monomers in ASU at very low resolution - 4.5A - and would like to ask two questions. - 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 would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I understand constrained NCS does not exist yet in phenix but is there something approximate that can be used in rigid body refinement ? I tried the conventional restrained NCS and the result was just like without restrains. Thank you for your time , Peter.
Hi Peter, here are a few considerations: - ADP refinement: use TLS combined with group B-factor refinement (one isotropic B per residue). It may be important to optimally define TLS groups. Use NCS. - coordinates: You may need to use custom bonds to restrain secondary structure elements. Use NCS. Note, you can define the strength of each NCS group individually. Just in case the automatic weight are not optional, try put more weight on geometry by using "wxc_scale=...". Yes, conventional rigid body refinement with small rigid groups may be good at some point, but may be too brutal as well, so constrained rigid body refinement (torsion angle dynamics) may be a good option. - mask: sometimes, using this "optimize_mask=true" makes a big difference at such resolutions, so you may want to try. - rigid body refinement is completely disconnected from the NCS restraints (no any restraints used during rigid body refinement). Pavel. On 10/15/09 1:12 PM, Peter Grey wrote:
Dear Phenix users,
I refine a large complex with three monomers in ASU at very low resolution - 4.5A - and would like to ask two questions. - 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 would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I understand constrained NCS does not exist yet in phenix but is there something approximate that can be used in rigid body refinement ? I tried the conventional restrained NCS and the result was just like without restrains.
Thank you for your time ,
Peter.
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
- 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
participants (3)
-
Pavel Afonine -
Peter Grey -
Phil Jeffrey