My suggestion was to compare the two routes starting from an atomic model, purely as a sanity check (and to answer your question).
This should avoid any issues to do with CTF, MTF etc.
Cheers
m
> -----Original Message-----
> From: Ardan Patwardhan [mailto:[log in to unmask]]
> Sent: 31 October 2013 12:08
> To: Winn, Martyn (STFC,DL,SC); [log in to unmask]
> Subject: RE: [ccpem] Correspondance between rotationally averaged power
> spectrum and SAXS curve
>
> Thanks Martyn
>
> Yes I found the structure factors bit quite confusing and your email
> helps clarify things.
>
> We have run CRYOSOL and calculated rotational power spectra for most
> EMDB entries. They can look quite different because of factors such as
> CTF, MTF etc but I wanted to know how similar I should expect them to
> look :)
>
> Best wishes
>
> -----Original Message-----
> From: Collaborative Computational Project in Electron cryo-Microscopy
> [mailto:[log in to unmask]] On Behalf Of Martyn Winn
> Sent: 31 October 2013 11:55
> To: [log in to unmask]
> Subject: Re: [ccpem] Correspondance between rotationally averaged power
> spectrum and SAXS curve
>
> There are certainly some issues here, and I am not sure I can give you
> a definitive answer. Your second link is to a page on liquid state
> theory, and I believe the term structure factor is used slightly
> differently there.
>
> For a start, I think the form factor is considered separately, so that
> the structure factor is purely for distance distributions irrespective
> of particle type (as in your quote). In contrast, the form factor is
> part of the structure factor used in crystallography, so different atom
> types are automatically included.
>
> As I understand it, the SAXS curve is an intensity curve. Thus the FT
> would give you distances, as in the Patterson function of
> crystallography. This is then what they call the "distance distribution
> function". It is clearly related in some way to the pair distribution
> function of liquid state theory, but I don't think it is quite the
> same.
>
> My hunch would be that (3) and (4) are the same (with the caveats
> listed by Sjors and Richard). Differential scattering (of X-rays or
> electrons) by different particle types must be included in both the EM
> volume and the SAXS curve, so I don't think that can be an issue. There
> may be some issues with appropriate normalisation?
>
> I guess the more practical approach is to just try it! crysol should
> give you a SAXS curve from an atomic model. You can make an EM volume
> from that atomic model, and then follow your procedure.
>
> HTH
> Martyn
>
> *
> * Dr. Martyn Winn
> * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
> * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH)
> * E-mail: [log in to unmask] Skype: martyn.winn
> *
>
>
>
> > -----Original Message-----
> > From: Collaborative Computational Project in Electron cryo-Microscopy
> > [mailto:[log in to unmask]] On Behalf Of Ardan Patwardhan
> > Sent: 31 October 2013 10:59
> > To: [log in to unmask]
> > Subject: Re: [ccpem] Correspondance between rotationally averaged
> > power spectrum and SAXS curve
> >
> > Dear Sjors and Richard
> >
> > Many thanks for your replies.
> >
> > There is still one thing that I am unclear about:
> > To calculate the radially averaged power spectrum
> > 1) Take the 3D density map and Fourier transform (FT) it
> > 2) Convert 3D FT to 3D power spectrum (PS)
> > 3) Radially average 3D PS to obtain 1D PS
> >
> > According to what I understand of SAXS
> > (http://en.wikipedia.org/wiki/Biological_small-angle_scattering but
> > also other sources): 4) the SAX scattering 1D curve is the FT of the
> > "distance distribution function". I understand that the FT of the
> > "distance distribution function"
> >
> (http://en.wikipedia.org/wiki/Radial_distribution_function#The_structu
> > r
> > e_fac
> > tor) under the assumption that "all particles are identical" is a
> > structure factor function.
> >
> > So for biological macromolecules, if we account for a) CTF, MTF
> > effects etc and b) the fact that the scattering cross sections will
> be
> > different for EM and X-rays, should we expect (3) and (4) to be the
> > same? Is the "all particles are identical" assumption valid even for
> > ribosomes and viruses where protein + DNA/RNA is present?
> >
> > Many thanks best wishes
> >
> > -----Original Message-----
> > From: RICHARD HENDERSON [mailto:[log in to unmask]]
> > Sent: 30 October 2013 19:20
> > To: Ardan Patwardhan; [log in to unmask]
> > Subject: Re: [ccpem] Correspondance between rotationally averaged
> > power spectrum and SAXS curve
> >
> > Ardan,
> >
> > Not identical, but definitely similar. The scattering cross-sections
> > are different for X-rays and electrons. Electron scattering is also
> > very sensitive to bonding (electron cloud radius) whereas X-ray
> > scattering is proportional to Z with a simpler form-factor.
> >
> > However, to the extent that C = N = O and hydrogen scatters less for
> > electrons and X-rays, they are similar.
> >
> > Richard
> >
> > On 30/10/2013 18:09, Ardan Patwardhan wrote:
> > > Dear all
> > >
> > > I was wondering if anyone could point me to a reference on the
> > > following
> > > question:
> > >
> > > Is the rotationally averaged power spectrum of a 3DEM
> reconstruction
> > > (in the absence of CTF effects etc) expected to be identical to a
> > > small angle X-ray scattering (SAXS) curve?
> > >
> > > Many thanks and best wishes
> > >
> > > Ardan Patwardhan
> > >
> > > European Bioinformatics Institute (EMBL-EBI) European Molecular
> > > Biology Laboratory
> > >
> > > Wellcome Trust Genome Campus
> > >
> > > Hinxton, Cambridge CB10 1SD, UK
> > > Tel: +44 1223 492649
> > >
> >
> > --
> > Richard Henderson
> > MRC Laboratory of Molecular Biology
> > Francis Crick Avenue
> > Cambridge Biomedical Campus
> > Cambridge CB2 0QH, U.K.
> > tel: +44-(0)1223-267065
> > fax: +44-(0)1223-268300
> > web: http://www2.mrc-lmb.cam.ac.uk/groups/rh15/
> >
> >
> > -----
> >
> > From Sjors:
> > Hi Ardan,
> >
> > No. Differences may for example arise from different MTFs of the
> > detectors used in the EM and X-ray experiments (or other envelope-
> > affecting factors).
> >
> > Sjors
> >
> > No virus found in this message.
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> > 10/30/13
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