[phenixbb] phenix auto sharpen local sharpening masking artifacts?

Oliver Clarke olibclarke at gmail.com
Thu Feb 1 08:46:12 PST 2018


I’m trying to run phenix.auto_sharpen with local sharpening, because I have an EM map that has a reasonably substantial variation in local resolution. This is the command I used:

phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26 local_sharpening=true local_aniso_in_local_sharpening=true model.pdb nproc=4 seq_file=seq.fasta >& log &

The resulting map looks beautiful (maybe a little too beautiful??) around the model, but shows some funky looking squared-off masking artifacts in the density further away from the model (in the micelle region). I tried to add a screenshot but the list wouldn’t let me. Am I doing something wrong? And can I trust that the density is completely free of model bias?


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