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

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

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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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