Hi Gunnar,
I would have thought that changing the value and gradient of the
target function had the potential to alter the minima?
Indeed, the target function is changed during the search, but
once a stable minimum is found, the DEN potential needs to
be zero by definition and the
Hi Rob,
This also means that the position of the minima of the target function
are not changed by the DEN (gamma=1) restraints.
I would have thought that changing the value and gradient of the
target function had the potential to alter the minima?
Indeed, the target function is changed
Hi Gunnar,
I generally agree with your comments. However, I'd like to clarify a couple of
points:
For gamma=1 the DEN potential can follow anywhere, the entire conformational
space is accessible and dij(t+1) depends only on Dij(t) and dij(t).
...
But, again, the starting (or reference)
Hi Rob,
thank you, your comments helped a lot.
From the Refmac5 paper I did not get the fact that d is set to d_current
after each step. In that case you are right, jelly-body corresponds rather to
DEN with gamma=1 than to gamma=0.
And of course, a very important difference is, as you
Hi Gunnar,
A couple of comments, to clarify a few of the similarities and dissimilarities
between DEN and analogous technologies:
According to your very nice paper from 2010, DEN refinement with gamma=0 gives
a higher weight to external information, whilst gamma=1 ignores external
information
Just a quick comment on low resolution refinement:
The concept of Deformable Elastic Network (DEN) refinement
is quite similar to jelly-body refinement in the special case of
gamma=0, for which the network is not deformable.
In contrast to jelly-body refinement, the DEN restraints are
however
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
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
Glad to clarify!
Also, note that whilst the springs between atoms analogy is nice for
visualisation purposes, and certainly helps to initially explain the concept,
it is not technically correct. Certainly, a similar analogy would be
appropriate for external restraints and NCS local restraints,
I know that refmac5 can run Jelly-body refinement for low resolution structure,
but how can I update my ccp4i to get the jelly-body refinement?
Thanks for all your suggestion.
by adding new external keywords as described as in the PDF described by
Garib N Murshudov
www.ccp4.ac.uk/schools/China-2011/talks/refmac_Shanghai.pdf
Padayatti PS
On Mon, Apr 25, 2011 at 5:19 AM, Zhipu Luo zhipu...@yahoo.com wrote:
I know that refmac5 can run Jelly-body refinement for low
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