I would like to have some comments on whether the maps before or after
truncation are better . (obviously the Rfactors will be lower for the
truncated data ..)
I suspect it iwill be completely anecdotal - but I confess to a gut
unhappiness about throwing out measurements..
eleanor
Pavel Afonine wrote:
> This is why phenix.refine by default outputs both maps: 2mFo-DFc
> "filled" and not "filled", and it is the best to look at both keeping
> in mind all pros and cons of each of them.
>
> Pavel.
>
>
> On 9/15/09 5:22 PM, Peter Zwart wrote:
>>> Application of a elliptical resolution boundary is justified because
>>> the
>>> resolution boundary from common integration programs (Denzo and
>>> Mosflm for
>>> example) is spherical where diffraction for anisotropic data is
>>> ellipsoidal.
>>> A spherical boundary would result in the inclusion of numerous poorly
>>> measured reflections in the higher resolution shells which
>>> effectively makes
>>> these data more noisy. Imposing an ellipsoidal resolution boundary is
>>> equivalent to removing noise from the higher resolution bins and is
>>> simply
>>> the anisotropic equivalent of the normal resolution limit truncation.
>>>
>>
>> Hi Justin,
>>
>> Please be careful in interpreting maps from elliptically truncated
>> maps, there is a potential for introducing some bias. In Refmac (as
>> well and Phenix) maps are produced that fill in missing amplitudes
>> with DFcalc. When your mtz file contains only a small fraction of
>> miller indices in the highest (spherical) shell, all the missing
>> reflections will be assigned DFcalc. Depending on your anisotropy,
>> this can be a significant number of reflections.
>>
>> I'm not sure how serious this issue is, but it might be worthwhile
>> checking the 'unfilled' maps as well (both phenix.refine and Refmac
>> allow you to compute these).
>>
>> HTH
>>
>> Peter
>>
>
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