[phenixbb] low resolution refinement question
Phil Jeffrey
pjeffrey at Princeton.EDU
Thu Oct 15 13:45:24 PDT 2009
> - 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
More information about the phenixbb
mailing list