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@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@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@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





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