Nudaurelia omega capensis virus (N omega V) capsids were previously characterized in two morphological forms, a T=4, 485-A-diameter round particle with large pores and a tightly sealed 395-A icosahedrally shaped particle with the same quasi-symmetric surface lattice. The large particle converts to the smaller particle when the pH is lowered from 7.6 to 5, and this activates an autocatalytic cleavage of the viral subunit at residue 570. Here we report that both 1-anilino-8 naphthalene sulfonate (ANS) and the covalent attachment of the thiol-reactive fluorophore, maleimide-ANS (MIANS), inhibit the structural transition and proteolysis at the lower pH. When ANS is exhaustively washed from the particles, the maturation proceeds normally; however, MIANS-modified particles are still inhibited after the same washing treatment, indicating that covalent attachment targets MIANS to a critical location for inhibition. Characterization of the low-pH MIANS product by electron cryo-microscopy (cryo-EM) and image reconstruction demonstrated a morphology intermediate between the two forms previously characterized. A pseudoatomic model of the intermediate configuration was generated by rigid body refinement of the X-ray structure of the subunits (previously determined in the assembled capsid) into the cryo-EM density, allowing a quantitative description of the inhibited intermediate and a hypothesis for the mechanism of the inhibition.