We study the connection between the chromospheric and photospheric behaviour of the active late-type star FK Comae. We use spot temperature modelling, light curve inversion based on narrow- and wide-band photometric measurements, Halpha observations from 1997-2010, and Doppler maps from 2004-2010 to compare the behaviour of chromospheric and photospheric features. Investigating low-resolution Halpha spectra we find that the changes in the chromosphere seem to happen mainly on a time scale longer than a few hours, but shorter variations were also observed. According to the Halpha measurements prominences are often found in the chromosphere that reach to more than a stellar radius and are stable for weeks, and which seem to be often, but not every time connected with dark photospheric spots. The rotational modulation of the Halpha emission seems to typically be anticorrelated with the light curve, but we did not find convincing evidence of a clear connection in the long-term trends of the Halpha emission and the brightness of the star. In addition, FK Com seems to be in an unusually quiet state in 2009-2010 with very little chromospheric activity and low spot contrast, that might indicate the long-term decrease of activity.
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