EMAN2 vs EMDB FSC calculation

[Jacob Croft]

Hello,

I recently noticed that when comparing (unmasked) FSCs plotted by EMAN2 vs calculated with the half maps on the EMDB web server (https://www.ebi.ac.uk/emdb/validation/fsc/) I get different results.

I have attached screenshots of both plots. As you can see, there is a bump in the FSC but it does fall down afterwards in the EMAN2 FSC, whereas in the EMDB FSC it never appear to dip back down.

Could you please help me interpret these results? I am worried this will cause a problem during submission.

Best,

Jake Croft

University of Washington

[Steve Ludtke]

I believe the EMDB server will use the masked 1/2 volumes for the FSC calculation, whereas, unless you applied the mask, the EMAN2 comparison is probably unmasked?

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<EMDB FSC.png><EMAN2 FSC.png>

[Jacob Croft]

Coming back to a related issue -

I was wondering if it is possible to get the unmasked/unfiltered half maps for earlier iterations of a e2spt_refine_new run?  For example, the threed_even_unmasked.mrc  and odd files that are output at the end are for the final iteration I believe (In this case threed_05), however I actually want to use and submit and earlier iteration (threed_03) that has a cleaner FSC and looks better because the final iteration looks overfitted.  However, the threed_03_even.hdf and odd maps look like they have been filtered, and I can't reproduce the FSC curves (fsc_unmasked_03.txt or fsc_masked_03.txt) using these half maps.  Is it possible to retroactively regenerate the unfiltered half maps from this iteration for submission to EMDB?).

Thanks!

Best,

Jake

[Steve Ludtke]

Hi Jake,

yeah, we don't keep all of the intermediate unmasked files to avoid eating so much disk space. You can regenerate the unmasked even/odd maps for an earlier iteration by rerunning the "make3d" jobs for that iteration. Just "grep make3d .eman2log.txt" and pick out the pair of lines for your iteration. You might want to change the output files, of course, to avoid overwriting the filtered versions.

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