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Additionally, the model-sharpening process provides a FSC for model vs map, and this FSC is a little higher for the half map in almost all resolution shells. Nice job on that…I tabulated and plotted the CC values vs d_min from auto sharpen… It confirms the full map is still mostly better than the half map, except past d_min 1.9.
I wonder if these higher frequencies are different in the two half maps, and average out when combining them.
in particular Figure 5B which shows how CC is not a good indicator at different resolutions.
Hi Greg, I had another look at two maps in question: emd_20026_half_map_2and emd_20026
Other than that, I wonder if you have the full map and half map 2 switched somehow - you mentioned you did it blind, could that be possible? Maybe..should be concluding that the full and half-maps at 1.8 A are not all that different (except for sharpening).
"Hi Cathy, I am checking out the maps for the challenge and it seems that the half-maps for 20026 are better than the full maps.If I run phenix.auto_sharpen on each of these, including a model in the auto-sharpen process (I docked 3ajo for this purpose), I get a very nice map in each case, but to me the model-sharpened map from half-map 2 is clearly better than the model-sharpened map from the full map (looking at the aromatic residues and definition of branched side chains which are much clearer in the model-sharpened half-map for example).I did this blind twice and each time I picked the model-sharpened half map over the model-sharpened full map.I used Chimera molmap to generate the model map, so nothing fancy. While the model_sharpened map now looks almost as good as the full map (I must have done it wrong before), it still looks just a little worse to me and has slightly lower Z-scores - see attached table.Would be interesting to see a similar analysis using the Phenix map-model CC calculations - I don’t think I know the internals enough to fully trust myself with that, or a way to automate it for many maps/models - will leave it for future consideration/discussion :) Greg To me, the emd_20026_half_map_2_model_sharpened_box_A.ccp4 map looks better than the emd_20026_model_sharpened_box_A.ccp4 map. What really impressed me is that sharpening the half map without a model produces an almost-as-good result as using the model!
About the previous message, I think that comparing CCs of a model in the same map (say at different resolutions of the model-map as you do in your paper) makes sense, but I still think it’s not robust/indicative of map quality to compare CCs of the same model in different maps - unless, perhaps, all map densities are first scaled to have the same mean/stdevs.