Hello All,
I think we are all in agreement that it depends on resolution, or more
specifically the amount of experimental data one has versus how many atoms one
has in the model to refine.
There is also no question that structures have become better over the decades
due to more and better rest
Hi All,
I believe it depends on the resolution. At sufficiently low resolution, it
may not be too unreasonable to assume that the main chain atoms of a
residue have the same B factors, and its side chain atoms also share the
same B factor (different from the main chain). Why? Simply because your
l
Hi Tom,I think restraints do change the data/parameter ratio, but how much is not straightforward. In, at least, the context of the Hamilton test restraints change the degrees of freedom which translates into a change of the effective data/parameter ratio. It is treated as adding extra observations
Hello Robbie,
Thanks for the stats and description of what has been done.
I think this puts us back into the realm of restraints versus constraints and
what is possible when trying to reduce the number of parameters to be refined.
Although grouped B-factors don't capture the reality of side chai
Hi Robbie and everyone,
Perhaps some clustering of the structure could be used to define TLS groups
rather than using chains. A spectral clustering based on Gaussian network model
normal modes seems to work fairly well for defining dynamical domains, for
example. In some cases these may be grou
Hi Tom,
At 3A the median number of reflections per atom is 3.4 which is indeed lower
than 4. So in unrestrained refinement the data/parameter ratio is indeed worse
than 1. This is where the effect of the restraints really matter and starting
from a flat B-factor model is interesting. This is wh
It appears that Zhonghao might be worried about his data to parameter ratio. At
3 A, one can easily be in a situation where one has fewer reflections than four
times the number of atoms (X, Y, Z plus B).
I like the idea of starting out with the average B (or even Wilson B) and then
doing TLS as
I thought it was possible to stop B values on bonded atoms from fluctuating
wildly?
But I am quite unable to follow the newly formatted documentation..
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One wonders who those "many people" are. You may not want to use them as your go-to reference for refinement techniques.Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic results. You are much
