I am a new PyMOL user trying to prepare figures for publication. I'm confused about the difference between the isomesh level of the 'mesh' in PyMOL and the contour level of the electron density map that I read in from CCP4. For example, for one of my figures I created a 3sigma Fo-Fc omit map and read it in to PyMOL. In order to make the density lovely I used the 'map_double' command and created a second 'mesh'. I then adjusted each of these 'mesh' to a 'level' of 4. Does this mean that my omit map is actually now contoured to 4sigma, or are the two not related?
Thanks for any help,