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CCPEM  September 2018

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Subject:

Re: Mass appearing outside of a mask in refinement

From:

Austin Dixon <[log in to unmask]>

Reply-To:

Austin Dixon <[log in to unmask]>

Date:

Tue, 11 Sep 2018 15:54:07 +0100

Content-Type:

text/plain

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Hi Daniel,

I'm a bit confused at what you've said concerning 'the original map after applying the mask'. My volume subtraction command was something to the effect of:

relion_image_handler --i original_protein_lowpass18.mrc --o region_of_interest.mrc --subtract without_region_of_interest_lowpass18.mrc

Where the volume passed to '--subtract' is a map of the '--i' map with the region of interest erased. The original map (entire protein) resolved to 4.2 Angstroms and looks quite clean. This focused refinement resolved to 5.5 at gold-standard FSC. Interestingly, upon further investigation it looks like the noise only appears after the two halves have converged and run_class001.mrc is created. All previous iterations have clean mass within the masked region.

Thanks,
Austin
Rockefeller University

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