Dear Steve and Martyn
Steve - thanks for the reference
Martyn - OK I misunderstood. We have not tried going both routes from an
atomic model but this would be a good sanity check and we will do that.
On the broader question of what we are doing and why?
We currently have a simulated SAX profile server (you can upload a map and
it will give you the SAXS profile) in testing and we are also calculating
the power spectrum and simulated SAXS profile for EMDB entries (again still
in testing). The idea to provide simulated SAXS profiles was discussed at
the Data management challenges in 3DEM meeting in 2011 (10.1038/nsmb.2426).
The "validation" aspect would be to be able to compare actual SAXS profiles
with the simulated one.
I don't expect there to be a big demand for the simulated SAXS server, but
for those who do - it will facilitate getting the data into EMDB. The
pre-calculated simulated SAXS profiles and rotationally averaged power
spectra for EMDB entries that we have looked at are in many cases remarkably
different and may provide useful insights for the wider EM community as a
part of our visual analysis pages.
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 13:05
To: [log in to unmask]
Subject: Re: [ccpem] Correspondance between rotationally averaged power
spectrum and SAXS curve
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
> >
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