[phenixbb] phenix.auto_sharpen expected filtration of input map

Ricardo Righetto ricardorighetto at gmail.com
Wed Jan 24 06:08:20 PST 2018


Hi Tom,

Yes, I meant the case with just a single map and a resolution value as
input.

Thanks a lot for the clarification!

Cheers,


--
Ricardo Diogo Righetto

2018-01-24 14:45 GMT+01:00 Tom Terwilliger <
tterwilliger at newmexicoconsortium.org>:

> Hi Ricardo,
>
> If you are using phenix.auto_sharpen with just a map and resolution as
> inputs, then it will (by default) apply an overall sharpening B-factor up
> to the resolution limit you supply, and then a blurring B-factor beyond
> that.  This means that any filtering applied to the input map will make a
> difference.  I haven't tested systematically, but my guess is that the
> better the map you start with with the better the map you'll get. So I
> would recommend starting with the weighted map as in Rosenthal and
> Henderson.  In this case phenix.auto_sharpen will basically be identifying
> the overall sharpening that optimizes the clarity and connectivity of the
> map.
>
> If you sharpen using a model, then a different sharpening is applied at
> each resolution (basically as in Rosenthal and Henderson, but based on the
> match between model and map, not between two half-maps), so the starting
> map should make only a small difference.
>
> All the best,
> Tom T
>
> On Wed, Jan 24, 2018 at 6:00 AM, Ricardo Righetto <
> ricardorighetto at gmail.com> wrote:
>
>> Hi,
>>
>> So far I have liked very much the results of phenix.auto_sharpen, but one
>> thing is not yet clear to me: how does it expect the input map to be
>> filtered?
>>
>> Would be something like:
>>
>> a) Unsharpened, unfiltered map (e.g. the simple average of the half-maps)
>> b) Unsharpened, SSNR-weighted (Cref) (Rosenthal & Henderson, JMB 2003)
>> c) Doesn't matter / other?
>>
>> Thanks in advance!
>>
>> Best wishes,
>>
>>
>> --
>> Ricardo Diogo Righetto
>>
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>
>
>
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> <https://maps.google.com/?q=100+Entrada+Dr,+Los+Alamos,+NM+87544&entry=gmail&source=g>
> Email: tterwilliger at newmexicoconsortium.org
> Tel: 505-431-0033
>
>
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