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?
Dept. Chemistry and Biochemistry
Arizona State University