[phenixbb] Local sharpening error

[Tom Terwilliger]

Hi Ricardo,
Yes, thanks that is a good idea. I will add the MW option.
All the best,
Tom T

On Thu, Jan 18, 2018 at 3:00 PM, Ricardo Righetto <ricardorighetto at gmail.com
> wrote:

> Hi Tom,
>
> Interesting approach. I agree that providing the sequence gives a more
> accurate volume estimation. May I suggest that alternatively the user could
> provide the MW and from that the volume could be estimated? This is how
> it's done in FREALIGN to calculate a volume-normalized FSC (Single-Particle
> Wiener filter).
>
> ps: I just ran the local sharpening with default parameters, providing the
> actual sequence and number of ncs_copies for my protein. It didn't take
> long but my volume is small (96x96x96), however it seems to be very
> over-sharpened in this particular case. The global sharpening on the other
> hand looks really nice!
>
> Thank you very much for the help.
>
> Best wishes,
>
>
> --
> Ricardo Diogo Righetto
>
> 2018-01-18 22:16 GMT+01:00 Tom Terwilliger <tterwilliger@
> newmexicoconsortium.org>:
>
>> Hi Ricardo,
>>
>> Yes, perfectly good question. The sequence is to guess the fraction of
>> volume occupied by the molecule. That in turn is used to try and segment
>> the map and figure out where the important parts of the map are located.
>> Those are where local sharpening is done.
>>
>> I should note that in my experience local sharpening in auto_sharpen only
>> occasionally helps beyond global sharpening and just takes a long time...
>>
>> All the best,
>> Tom T
>>
>> On Thu, Jan 18, 2018 at 1:59 PM, Ricardo Righetto <
>> ricardorighetto at gmail.com> wrote:
>>
>>> OK Tom, thanks a lot for the very quick reply! I'll try that.
>>>
>>> But now I'd like to understand - why is the sequence file necessary at
>>> all? I thought the local sharpening approach just did the same as the
>>> global sharpening, only sliding a small box throughout the volume. It seems
>>> then that this is not the case?
>>>
>>> Best wishes,
>>>
>>>
>>> --
>>> Ricardo Diogo Righetto
>>>
>>> 2018-01-18 21:53 GMT+01:00 Tom Terwilliger <
>>> tterwilliger at newmexicoconsortium.org>:
>>>
>>>> Hi Ricardo,
>>>>
>>>> I'm sorry, yes you do have to supply a sequence file for local
>>>> sharpening.  I will fix the documentation.  If you want you can just put in
>>>> a dummy sequence and supply a value for "solvent_content=xxx" and that will
>>>> accomplish the same thing.
>>>>
>>>> Let me know if that doesn't do it!
>>>> all the best,
>>>> Tom T
>>>>
>>>> On Thu, Jan 18, 2018 at 1:42 PM, Ricardo Righetto <
>>>> ricardorighetto at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am trying to do local sharpening with phenix.auto_sharpen, with the
>>>>> following command:
>>>>>
>>>>> phenix.auto_sharpen map.mrc resolution=4.0 local_sharpening=True
>>>>>
>>>>> Then it runs the global sharpening first as expected, but when it gets
>>>>> to the local sharpening it crashes with the following error:
>>>>>
>>>>> Sorry: Please specify a sequence file with seq_file=myseq.seq
>>>>>
>>>>> Nowhere it says that I would need a .seq file in order to do local
>>>>> sharpening (global sharpening works fine). Any ideas?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> --
>>>>> 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 <(505)%20431-0033>
>>>>
>>>>
>>>
>>
>>
>> --
>> 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 <(505)%20431-0033>
>>
>>
>


-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0033
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