Garib gave a nice description of jelly-body refinement at the ACA
meeting. IIRC from his talk, conceptually jelly-body refinment is the
equivalent of adding "springs" between atoms within a certain radius of
each other that restrain their movement during refinement. The
restraints contribute to the target function curvature. The weight
factor describes the contribution of the restraints to the overall
target function. If w=1 and and the radius of atoms considered was
infinity, you would have rigid body refinment. If w=0 you have normal
uncontrained refinment. The REFMAC defaults are 4.2 A for the
constraints radius, and 0.02 for the weighting factor. If I understand
it correctly, it's basically like a slightly flexible rigid body
refinement. Bigger w, more rigid jellyfish. (Someone will correct me if
I have this wrong.)
Mathematically, the contribution to the target function is sum(w
(|d|-|dcurrent|)^2) where is d is a measure of the distances between
atom pairs within a certain radius. The value d is the new distances and
dcurrent is the old distances. The value w is the weighting factor.
I have a recently obtained 2.9A dataset for which this approach might be
interesting to try and see how it works compared to the usual
unrestrained refinement and/or TLS, etc.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [email protected]
On 8/23/2012 1:27 PM, Nathan Pollock wrote:
Dear experts,
Could someone explain what it is exactly that jelly body refinement
does? I think that I understand it intuitively but want to make sure.
In the same vein, what does jelly body refinement sigma parameter
control? I.e., in comparison to the default sigma = 0.02, does sigma =
0.1 make body more or less like a jelly fish?
Thanks!
- Nate
