Re: [ccp4bb] Looking at an EM map..
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 well as positive. For electron diffraction in a simplified form there is a relationship (and it is used in some programs, including refmac) between X-ray and electron scattering factors. Using the fact that electron density and electrostatic potential are related by Poisson equation Mott-Bethe derived a formula: f_e(s) PropTo (Z-f_X(s))/s^2 Z is nuclear charge and f_x(s) is X-ray form factor (Fourier transformation of spherical form of electron density of an atom. f_x(0) is the total number of electrons. For charged atoms at s=0 Z-f_X(s) is different from 0 and therefore for positively charged atoms it could be very large positive number. and for negatively charged atom it could be very negative number. (There is screening effect related to realignment of charges around charges also, but still negatively charged atoms will have negative scattering factors at low resolution). At higher resolution all scattering factors become positive. So, if you measurement (density) is at low resolution then density map can be negative. It is true for EM as well as electron diffraction. There is an additional complications in EM when you compare maps from reconstruction to the atomic electrostatic potential: maps have been subjected to some filtering procedure. An additional complication in density maps after scattering experiment is that scattered particles can knock out some hydrogens (eventually knocking out some of atoms or group of atoms) and the result could be an accumulation of negative charges and therefore (at low resolution) weakening of maps, in some cases making them negative. There are few more complications (direction dependence, solvent behaviour, dynamic scattering effects etc). Regards Garib P.S. I am sorry that this mail turned out to be longer than I wanted. On 15 Mar 2018, at 14:41, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > So if I calculate "structure factors" from a map do I just use the map as is > with the negative values included ? > > Eleanor > > On 15 March 2018 at 14:37, Ian Tickle wrote: > > 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 > > -- Ian > > On 15 March 2018 at 14:17, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 > > Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
Re: [ccp4bb] Looking at an EM map..
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 maps, fundamentally different from electron density maps in X-ray crystallography. All the best, Steve On Thu, Mar 15, 2018 at 12:09 PM Pavel Afonine wrote: > 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 ARG > and LYS (positively charged NH1, NH2, NZ), and all other side-chain atoms. > Clearly side-chain oxygen atoms of ASP and GLU have indeed systematically > weaker density: > > http://cci.lbl.gov/~afonine/tmp/fig.png > > First picture: all maps from EMDB of resolution 3A or better. Second > picture: all maps from EMDB of resolution 3-4A. > > All the best, > Pavel > > On Thu, Mar 15, 2018 at 7:17 AM, Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> 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 >> > > -- Steve Chou
Re: [ccp4bb] Looking at an EM map..
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 ARG and LYS (positively charged NH1, NH2, NZ), and all other side-chain atoms. Clearly side-chain oxygen atoms of ASP and GLU have indeed systematically weaker density: http://cci.lbl.gov/~afonine/tmp/fig.png First picture: all maps from EMDB of resolution 3A or better. Second picture: all maps from EMDB of resolution 3-4A. All the best, Pavel On Thu, Mar 15, 2018 at 7:17 AM, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 >
Re: [ccp4bb] Looking at an EM map..
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 included ? > > Eleanor > > On 15 March 2018 at 14:37, Ian Tickle wrote: > >> >> 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 >> >> -- Ian >> >> On 15 March 2018 at 14:17, Eleanor Dodson <176a9d5ebad7-dmarc-reques >> t...@jiscmail.ac.uk> wrote: >> >>> 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 >>> >> >> >
Re: [ccp4bb] Looking at an EM map..
So if I calculate "structure factors" from a map do I just use the map as is with the negative values included ? Eleanor On 15 March 2018 at 14:37, Ian Tickle wrote: > > 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 > > -- Ian > > On 15 March 2018 at 14:17, Eleanor Dodson <176a9d5ebad7-dmarc- > requ...@jiscmail.ac.uk> wrote: > >> 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 >> > >
Re: [ccp4bb] Looking at an EM map..
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 -- Ian On 15 March 2018 at 14:17, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 >
[ccp4bb] Looking at an EM map..
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