On Friday, January 06, 2012 11:15:11 am Ed Pozharski wrote:
> On Fri, 2012-01-06 at 10:48 -0800, Ethan Merritt wrote:
> >
> > A TLS model is more likely to be appropriate.
>
> A quick clarification request if I may:
>
> We all seen how well the multi-group TLS models seem to match the
> B-factor variation along the chain. Is this in your opinion how such
> model may be really effective, by incorporating most of the B-factor
> variation into ~100 TLS parameters?
I have run statistical analysis of alternative models on various
structures in the resolution range 2.8 - 4.0 A. For some of these,
I found that a full 1-Biso-per-atom model was indeed statistically
justified. For most, however, a TLS model was better. For some,
a hybrid Biso + TLS model was better than either alone. So this really
should be decided on a case by case basis rather than trying to come
up with a single "rule of thumb".
Now as to how many TLS groups a model should be partitioned into, that
varies all over the place and is clearly a consequence of the individual
lattice packing. For some structures with loose packing (as I interpret
the cause), a single-group TLS model with uniform constant per-atom B
is significantly better than a model with a separate B factor for each
atom but no TLS component. Adding additional TLS groups does not actually
help that much. To me this means that the largest factor contributing to
the ADPs is the overall displacement of the whole molecule within the
lattice, which is strongly anisotropic. The single-group TLS model
describes this anisotropy well enough, while any number of isotropic B
factors does not.
Those cases where the individual B factor option tests out best correspond,
as I interpret it, to relatively rigid lattice packing. In these crystals
the overall anisotropy is very low, so TLS models are not the right
formalism to use in describing the distribution of ADPs. Perhaps
normal-mode models would be better; it is hard to draw conclusions from
the very small number of normal-mode refinements reported to date.
> And a question:
>
> Given that the B-factors for side chain atoms will be generally higher,
> do you know if creating two separate sets of TLS parameters for
> backbone / side chains improves things?
That is a question that I am currently working on. I don't think that
two sets of TLS parameters will turn out to be a good way to handle it.
I am more attracted to the idea of applying a TLS description on top of
a fixed a priori model for B variation along the sidechain. This
approach is inspired by the per-amino acid targets for varying B along
the sidechain that were developed by Dale Tronrud for use in TNT.
cheers,
Ethan
> Thanks,
>
> Ed.
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
