I've been using pymol for quite some time now but the contour level is still a mystery to me.  Why is there a difference bewteen contour levels of FFT electron density maps displayed in Xfit vs pymol?  When using the command for example :isomesh mesh1, fo-fc, 1.0, etc..., in pymol what does 1.0 in terms of sigma level really mean.  I was under the assumption that 1.0 sigma is equal to 1.0 sigma as defined by FFT, but then there would not be a difference in the two maps displayed at this value in the two programs, which there is.  Can anyone help clarify this issue?
Much gratitude,

Gabrielle Malo
Dept. Chemistry and Biochemistry
Arizona State University