Hi Oli, I am sorry for the trouble with phenix.map_sharpening! I think that the problem is the lack of clarity on our part about how to specify the sequence file. You need to use "seq_file=seq.fasta" and not sequence_files=seq.fasta. Once you fix that you will see that you need to specify one more thing...if you supply a single map you now need to say "sharpening_method=b-factor" to differentiate between shell-scaling (was phenix.aniso_sharpen) and b-factor scaling (was phenix.auto_sharpen). (In the GUI this is supposed to be more clear...) So your command now is: phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 \ seq_file=seq.fasta sharpening_method=b-factor Let me know if that does not do it! All the best, Tom T b-factor scaling On Tue, Jun 3, 2025 at 2:15 AM Oliver Clarke wrote:

Actually - there seems to be some other problem here, because even if I provide a sequence file - e.g. phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 sequence_files=seq.fasta - it seems to read the sequence file, but still terminates complaining about the absence of a sequence. This is using phenix-2.0rc1-5668.

Cheers Oli

...

On Jun 3, 2025, at 9:54 AM, Oliver Clarke 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

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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 Email: [email protected] Tel: 505-431-0010

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