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On 11/21/2014 12:35 AM, "F.Xavier Gomis-Rüth" wrote:
> <snip...>
>
> As to the convenience of carrying over a test set to another
> dataset, Eleanor made a suggestion to circumvent this necessity
> some time ago: pass your coordinates through pdbset and add some
> noise before refinement:
>
> pdbset xyzin xx.pdb xyzout yy.pdb <<eof noise 0.4 eof
>
I've heard this "debiasing" procedure proposed before, but I've
never seen a proper test showing that it works. I'm concerned that
this will not erase the influence of low resolution reflections that
were in the old working set but are now in the new test set. While
adding 0.4 A gaussian noise to a model would cause large changes to
the 2 A structure factors I doubt it would do much to those at 10 A.
It seems to me that one would have to have random, but correlated,
shifts in atomic parameters to affect the low resolution data - waves
of displacements, sometimes to the left and other times to the right.
You would need, of course, a superposition of such waves that span
all the scales of resolution in the data set.
Has anyone looked at the pdbset jiggling results and shown that the
low resolution data are scrambled?
Dale Tronrud
> Xavier
>
> On 20/11/14 11:43 PM, Keller, Jacob wrote:
>> Dear Crystallographers,
>>
>> I thought that for reliable values for Rfree, one needs only to
>> satisfy counting statistics, and therefore using at most a couple
>> thousand reflections should always be sufficient. Almost always,
>> however, some seemingly-arbitrary percentage of reflections is
>> used, say 5%. Is there any rationale for using a percentage
>> rather than some absolute number like 1000?
>>
>> All the best,
>>
>> Jacob
>>
>> ******************************************* Jacob Pearson Keller,
>> PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr,
>> Ashburn, VA 20147 email: [log in to unmask]
>> ******************************************* .
>>
>
> --
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