[phenixbb] Re: phenix.map_sharpening - sequence file required?

Fantastic, thanks so much Tom!! Cheers Oli

On Jun 3, 2025, at 6:08 PM, Tom Terwilliger wrote:

Hi Oli,

Thanks for pointing this out! I have now fixed phenix.map_sharpening so that:

1. You can supply either molecular_mass or sequence file if you are using b-factor sharpening (as in the previous phenix.auto_sharpen).

2. You do not need to specify either if you are using shell sharpening (as in previous phenix.aniso_sharpen).

I also fixed the error messages so that they tell you what to type in (e.g., seq_file=seq.fasta)

These will be available in tomorrow's nightly build/release candidate.

Let me know if this does not do it! All the best, Tom T

On Tue, Jun 3, 2025 at 1:55 AM Oliver Clarke mailto:[email protected]> wrote:

...

Hi,

The new-ish map_sharpening utility seems to absolutely require a sequence file (at least on the CLI), whereas using auto_sharpen one could directly provide solvent content or estimated molecular mass.

This option - molecular_mass - is still present in map_sharpening, but the program still terminates with an error - "Sorry: Need a sequence file". Is this intended?

I run using the following command: phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 molecular_mass=50000

Cheers Oli _______________________________________________ phenixbb mailing list -- [email protected] mailto:[email protected] To unsubscribe send an email to [email protected] mailto:[email protected] Unsubscribe: phenixbb-leave@%(host_name)s

-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] mailto:[email protected] Tel: 505-431-0010