[3dem] creating models from PDB files

Sigworth Fred fred.sigworth at yale.edu
Thu Jul 28 14:20:13 PDT 2011


Dear David,

As Matthias mentioned, we have been concerned with getting the solvation right.  For making realistic models for comparison with data or testing reconstruction programs, it is very important not to simulate the protein in vacuum, which is what one gets by just putting density at the position of each atom in the pdb file.  Because water matches the protein density fairly well, adding the water density makes a big difference in simulated images.  Based on work in the X-ray field we have been experimenting with simple solvation models and have had some success in making models from pdb files that reproduce what we see in MD simulations.

Fred Sigworth



Fred J. Sigworth
Professor
Department of Cellular and Molecular Physiology
Yale School of Medicine
333 Cedar Street
New Haven, CT  06520
fred.sigworth at yale.edu
203 785 5773



On Jul 27, 2011, at 3:47 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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