[3dem] creating models from PDB files

[Penczek, Pawel A]

Hi,

I spent significant amount of time testing various approaches to conversion of pdb models
to discretized EM density maps, but could not come up with a result that would be significantly
better than simple tri-linear interpolation implemented in spider or sparx.  This scheme also has a significant advantage
of being very fast.

Schemes that use Gaussian priors tend to produce maps that look "smoother", but for larger pixel sizes
there is no noticeable difference in comparison with the simple scheme.

Generally, the problem with "sophisticated" schemes developed for crystallography is that (a) they
target very high resolution structures and (b) mimic effects and image formation mechanisms that
are not necessarily relevant for EM.  One may also add that inaccuracies of EM maps, even those 
done at near-atomic resolution, outweigh inaccuracies of pdb conversion schemes by a large margin.

Regards,
Pawel.

On Jul 27, 2011, at 9:47 PM, David Gene Morgan wrote:

> Hi,
> 
> 	Has anyone done any sort of critical evaluation of the different 
> programs that will read PDB files and generate volumes?  I know that 
> there are lots of ways to do this, and that different programs appear to 
> do fairly different things.  But does anyone have good reasons for 
> believing that one program is better than another?
> 
> -- 
>                  David Gene Morgan
>                   cryoEM Facility
>                   320C Simon Hall
>            Indiana University Bloomington
>                812 856 1457 (office)
>                812 856 3221 (EM lab)
>             http://bio.indiana.edu/~cryo
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