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

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 :

...

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 < [email protected]> 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- 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: [email protected] 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: [email protected] Tel: 505-431-0033

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

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 :

...

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 < [email protected]> 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 < [email protected]>:

...

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 < [email protected]> 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- 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: [email protected] 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: [email protected] 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: [email protected] Tel: 505-431-0033