Hi Oli, Try adding the keyword "map_file_name": phenix.mtriage map_file_name=my_map.ccp4 Let me know if that doesn't do it! All the best, Tom On Sat, May 26, 2018 at 2:44 PM, Oliver Clarke wrote:

Ah right, thanks Ricardo!

I thought that might be the case, but there was nothing in the command line help or online docs to indicate it, and whenever I attempt to run phenix.mtriage, I get the error "Sorry: No box info (aka crystal symmetry) available”, even when I run it on the map generated by phenix.auto_sharpen. There also doesn’t seem to be any option to provide this info on the command line (except in the form of a model, I guess).

Cheers Oli

On May 26, 2018, at 3:35 PM, Ricardo Righetto wrote:

Dear Oli,

The d99 criterion is available in the phenix.mtriage program.

Best wishes,

-- Ricardo Diogo Righetto

2018-05-26 20:44 GMT+02:00 Oliver Clarke :

...

Hi,

I think the “d99” criterion described in this preprint ( https://www.biorxiv.org/content/early/2018/03/14/279844) looks like a really interesting FSC-independent way to measure res in real space, and I’d like to give it a go on my maps (particularly those where I am suspicious of the FSC-based res based on map appearance, or where I suspect overfitting).

Is it available in any phenix package at present? The scripts site mentioned in the preprint (http://phenix-online.org/phen ix_data/afonine/cryoem_validation/) is currently rather sparsely populated.

(Also, I wonder whether a directional version of the d99 criterion might be useful to estimate anisotropic res in the case of a preferred orientation, analogous to the 3D-FSC approach of Yong-Zi Tan and Dmitry Lyumkis?)

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

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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: 505-431-0033