Re: [PyMOL] contour levels in pymol

[Peter A. M. <pa...@co...>]

> 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?

I was confused about this myself a few months back.  The sigma level comes
from the rms deviation of the map, not the fft itself.  So if the maps are
different (different sizes, covering different regions, or calculated
using different grid spacints), then the sigma levels won't necessariily
be equivalent.

If all of the map parameters are the same and you still get differences in
the displayed maps for the two programs, then there's something else going
on.

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University