Re: [ccp4bb] Looking at an EM map..

2018-03-16 Thread Garib Murshudov
Yes. that is how it should be done. if you have a map then you convert them to Fourier coefficients directly using Fourier transformation. Only for some particles density maps are positive everywhere. X-ray particles are one of them. For neutron and electron scattering maps could be negative as

Re: [ccp4bb] Looking at an EM map..

2018-03-15 Thread Steve Chou
EM maps are electron potential maps, fundamentally different from electron density maps in X-ray crystallography. You might also want to check the Protein Science paper by Jimin Wang & Peter Moore, 2017 http://onlinelibrary.wiley.com/doi/10.1002/pro.3060/abstract EM maps are electron potential

Re: [ccp4bb] Looking at an EM map..

2018-03-15 Thread Pavel Afonine
This is discussed, for example, here: http://www.pnas.org/content/114/12/3103 Also, here I calculated the distribution of map values (scaled in r.m.s.) for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of

Re: [ccp4bb] Looking at an EM map..

2018-03-15 Thread Ian Tickle
I would say so yes, but Garib is the expert on this - I'm only repeating what he told me! Cheers -- Ian On 15 March 2018 at 14:41, Eleanor Dodson wrote: > So if I calculate "structure factors" from a map do I just use the map as > is with the negative values

Re: [ccp4bb] Looking at an EM map..

2018-03-15 Thread Ian Tickle
Hi Eleanor Electron scattering factors can be negative for negative ions, particularly at low d*. For a low-resolution map it means that the electric potential is the opposite sign to what you expected. It's why you often don't see ASP & GLU side-chains in low resolution EM maps. Cheers --

[ccp4bb] Looking at an EM map..

2018-03-15 Thread Eleanor Dodson
I am pig-ignorant about these ,, but this example has negative values as well as positive.. What does this mean? I thought a well phased map would be pretty well all positive.. Eleanor