[3dem] simulated micrograph for ctf determination?

[Friedrich Foerster]

in small angle x-ray solution scattering effective form factors are
used that take care of the average solvent effect. these form factors
'remove' the contribution of the excluded solvent from the vacuum
contribution. to low resolution (2 nm) the angular dependence of the
form factor is negligible. the same strategy should also work for em
if you want to account for the solvent effect (excluding a possibly
ordered hydration shell). thus, when simulating an em map a quick and
dirty solution to include the major solvent effect would be to just
use these effective f(0)s instead of the vacuum f(0)s (or atomic
number or mass, which are approximately proportional).
for the actual parametrization look at:

Fraser, R., MacRae, T., and Suzuki, E. (1978) An improved method for
calculating the contribution of solvent to the X-ray diffraction
pattern of biological molecules. J. Appl. Crystallogr. 11:693-4.

best

friedrich

On Wed, Sep 16, 2009 at 3:10 AM, Fred Sigworth <fred.sigworth at yale.edu> wrote:
> Making random projections, operating with CTF and adding noise is
> straightforward with any of several software packages (I can even give you a
> script in Matlab!).  But, there is a critical problem for which I haven't
> seen a solution.  This is the problem of solvating the macromolecule.  If
> you just take the pdb coordinates to create a density map, you will have a
> model of protein in a vacuum, which has a much higher-contrast molecular
> boundary than the actual molecule solvated in water.
> Does anyone have a solution to this problem?  To get a realistic model of a
> streptavidin tetramer, we wound up doing a molecular dynamics simulation (L.
> Wang et al., J. Struct. Biol. 2008, PMID: 18707004).  Using VMD Liguo Wang
> put the molecule into a box of water molecules, and then ran an MD
> simulation using NAMD for about a nanosecond to allow waters to find good
> positions.
> -Fred Sigworth
>

--

Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2651
Fax: +49 89 8578 2641

foerster at biochem.mpg.de

www.biochem.mpg.de/foerster