Hello,
 
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

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Gabrielle Malo
Dept. Chemistry and Biochemistry
Arizona State University
(480)727-7843
gmalo@asu.edu