Dear Colleagues, I am preparing to deposit a cryo-EM structure to EMDB/PDB and have encountered an important question regarding resolution reporting and half-map deposition after Phenix density modification. My Situation: 1. I performed 3D refinement in CryoSPARC, generating two independent half-maps 2. I calculated FSC between these original half-maps at the 0.143 threshold: X Å resolution. 3. I processed these half-maps through Phenix resolve_cryo_em for density modification 4. Phenix reports improved resolution of Y Å (based on corrected FSC as documented in your resolve_cryo_em guide) 5. I generated the corresponding FSC XML file from Phenix showing Y Å Questions: When I deposit to EMDB, I understand the policy requires depositing the original, unmodified half-maps (unfiltered, unmasked, unsharpened). However, when EMDB validates the deposition by independently recalculating FSC from these half-maps, they will obtain X Å, not Y Å. This creates an apparent contradiction: • Deposited FSC XML file: Y Å (from Phenix) • EMDB independent FSC calculation from deposited half-maps: X Å (from originals) * When you apply corrections for correlations introduced by density modification in resolve_cryo_em, does this mean the Y Å resolution should be reported as the official resolution, even though the original half-maps show X Å? * What is the recommended workflow when depositing density-modified maps to ensure consistency and avoid validation conflicts? Additionally: • No atomic model was used; only sequence information • The density modification improved map quality and interpretability as intended Thank you. Kind regards, Dmitry