"MULTISCALE manual; anisotropic scaling +
nissen at KEMI.AAU.DK
Fri Mar 7 10:13:19 EST 1997
I have had a very similar case refining a protein-RNA complex at 40-2.9
resolution with X-PLOR. Too, I had great advantage of applying both
scaling and a bulk-solvent correction. Further, I also got a steady
the overall B upon successive rounds of these corrections after
cycles. What you may probably see, is that the Rfree against your native
(no anisotropic scaling, no bulk solvent corr.) has increased.
bulk solvent model is modelled to account for more and more of the
the model with increased B-factors accounts for less and less.
I came over this problem in the following way:
The model coordinates + B were subjected to overall B-factor (all atoms
and grouped B-factor refinement (mainchain, sidechain, phospho-ribose,
against the native data (9-2.9 A), followed by anisotropic scaling
(9-2.9 A 2sigma cutoff in scaling, 40-2.9 A output) and bulk solvent
(40-2.9 A). Finally, the model coordinates and B-factors were subjected
B-factor refinement (40-2.9 A) against the new corrected dataset (ani. +
This corrected dataset and latest B-factor refined model was used for
and the proceeding refinement job was performed with those corrected
In this way, the successive increase of the overall B is avoided, and
one can on each modelbuilding/refinement cycle check Rfree against the
native data, independent
of corrections based on the model itself (almost, at least....).
In my case, Rfree dropped by typically 5% upon anisotropic scaling and
correction. However, I was most concerned with the Rfree calculated
native data. This was my true measure of phase-improvement.
Note, that the "baoverall.inp" should be slightly changed, so that you
use the higher resolution data for the anisotropic scaling, while
this scaling to the low resolution data also (use two d_min cutoff
d_min_scale and d_min_out).
I have tested different scenarios of this cycle and have found that the
order of corrections is the best (e.g. bulk solvent corr. followed by
scaling leads to miscorrections). Further, I have tested the effect of
different sigma cutoffs in the anisotropic scaling and have found that a
2 sigma is optimal.
Laboratory of Macromolecular Crystallography
Institute of Molecular and Structural Biology
More information about the X-plor