Dear authors,

Thank you for the revised version of your GMD manuscript "Assimilating Compact Phase Space Retrievals of Atmospheric Composition with WRF-Chem/DART: A Regional Chemical Transport/Ensemble Kalman Filter Data Assimilation System" (gmd-2015-116). Before accepting your manuscript for publication, I would like to ask you to take into account point number 2 raised by reviewer #1 in reply to your "author's response" (please see list below). I am expecting your manuscript to be ready for publication in GMD then.

Thank you,

Axel Lauer
(handling topical editor)

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1) Agreed
2) I have now realized that my comment was based on a misinterpretation of the meaning of E_m in Eq. 3. I was under the impression that with E_m the authors meant the observation error covariance matrix. This symbol is indeed one of those normally used to indicate this quantity in the relevant literature. I now agree with the authors’ reply given that with E_m they actually mean the measurement error covariance in retrieval space (despite in their reply they keep calling it the observation error covariance). I note however that in the paper at the end of section 5 another term is used for the same quantity, namely C_m, adding to the confusion. I would suggest that the symbol C_m is used instead of E_m throughout the paper.
3) Agreed
4) I now agree with the authors given that E_m actually represent in their paper the measurement error covariance in retrieval space rather than the measurement error covariance as I originally thought.
5) I am satisfied with the authors’ reply and proposed changes to the paper.