Maybe we could invent an R_Schrodinger that hovers in a quantum state untill we
peek :)
J
William Scott <[EMAIL PROTECTED]> wrote:>
> If R-sleep is to be the "real" validation R-factor, why not just
> sequester
> each of R-sleep and the current R-free, each as a randomly-chosen (but
> mutually
Does Refmac prints this value (observations (with restraints) over
parameter) somewhere in the log file? Maybe it does, and I just cannot
find it. However, I do find the numbers of observation, restraints and
atoms, so it is easy to calculate manually. But wouldn't it be useful to
have this val
I have a vacancy for Team Leader for Infrastructure and Methods
Development in my group that is still being advertised; this is the
Protein Crystallography group of the Structural Genomics Consortium,
Oxford.
For details, please see: http://www.sgc.ox.ac.uk/jobs/07079.html, and
feel free to
Dear All,
I would argue that there are very few situations where it is
necessary to use R-free as a criterion for optimization (as opposed
to R-work). In any case where the parameterization is fixed and we
are simply looking for the best set, R-work will do just fine. It is
only situations
Sue,
I have the following 4 lines in /etc/rc.local:
if [ ! -e /lib/modules/`uname -r`/kernel/drivers/video/nvidia.ko ]; then
echo "installing NVIDIA kernel module. This takes some time."
/root/NVIDIA.run --no-network -s -K -n
fi
This automagically recompiles the module after a kernel upda
If R-sleep is to be the "real" validation R-factor, why not just sequester
each of R-sleep and the current R-free, each as a randomly-chosen (but
mutually exclusive) set of reflections, and then proceed as normally with
the other (eg) 80% of the data until the very end of the refinement, using
the
On Monday 01 October 2007 08:49, Peter Adrian Meyer wrote:
> This raises a slightly tangential question though - how do we know how
> what obs/param ratio is good enough? My understanding was that obs/param
> of 1 was sufficient for linear systems
This is wrong, unless by "sufficient" you only me
This raises a slightly tangential question though - how do we know how
what obs/param ratio is good enough? My understanding was that obs/param
of 1 was sufficient for linear systems; but it doesn't seem that any of
the objective functions used for refinement are linear (and I haven't been
able to
Hi Peter
It has nothing to do with linear vs. non-linear models, it has everything to do
with errors in the data and the model. Sure, if there are no errors you can in
general solve for N unknowns exactly from N equations (obs/param ratio = 1)
whether there's a linear relationship or not (thou
I haven't read the paper, so perhaps shouldn't say anything yet, but
here goes.
For me Rfree is primarily a tool to help choose the refinement protocol,
set the relative weight for geometry restraints versus crystallographic
data, B-value restraints etc. Trying different parameter settings and
Just to add that the R-free and R-sleep are nothing else than what is
'officially' known as 'test' set and 'validation' set.
In statistical pattern recognition for example, one would use a
'training' set to establish the 'model'; the power of the model
(in this case the 'model' can be for examp
To clear up a few things.
International support is extremely welcome.
Commercial organization support is extremely welcome.
In fact both of these are essential and will count for more than UK
academics.
ANY letter of support from ANYONE is welcome.
Step change, paradigm shifting are anglosaxo
The question is how significant is this bias, and is the cure (i.e. leaving out
more reflections from the working set) worse than the disease? For refinements
at 'medium' typical resolution (around 2.5 to 2 Ang) we are working with an
observation/parameter count ratio of say < 3 (naturally I'm
Dear All,
the short paper by Gerard Kleywegt (ActaD 63, 939-940) treats an
interesting subject (at least I think so...). I agree that what we
are now doing in many cases is effectively refining against Rfree.
For example, the standard CNS torsion angle refinement does n
refinement trials
Dear Colleagues,
CCP4 derives its core financial support from the
BBSRC (UK). We are now in the process of attempting to renew our grant
funding. The grant proposal has four sections
(1) New methods for working with low resolution and difficult structures
(2) Improvements in
There are two ways -
1) Import both sets - combine using CAD ( it is the first task of the
Experimental phasing module) - do the automatic checking that you have
the same indexing conventions -
Scale data sets together ( 2nd task of Experimental phasing module) -
that will give an R factor betw
Is this possible?
Currently I have two crystal data's. I have been importing the scaled averaged
files using d*trek.
The only difference between the two crystals is that one has been soaked with a
ligand. Now I want to see if it is there.
Is there a way to import both sets of data at the same
Yes to keeping the same FreeR
Bfactors - I doubt if it matters, but I usually start a new data set by
setting Bs to the Wilson suggestion..
Twinned data - maybe you ought to use SHELXL to refine it?
Eleanor
john kryst wrote:
Hi all !!
I am working on some deletion mutants. Mutant
You can just set your default FreeR value to 1.
See the REFMAC gui etc..
Eleanor
Petra Lukacik wrote:
I have a mtz file (output from phenix AutoSol and AutoBuild) where the
FreeR flag for the test set has a value of 1 and and the working set
has value 0. This is opposite to the ccp4 default wh
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