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 _______________________________________________
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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
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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