[3dem] creating models from PDB files

[Matthias Wolf]

Hi Dave,

I don't know how much it really matters to have "correct" density, but as our 
technique has reached near-atomic resolution, it seems adequate to use proven 
methods that result in superior density than from a "bunch of spheres". This 
applies in particular if such a model-derived density is used to scale 
experimental maps.
Wang & Sigworth (JSB, 2008, Nature 2009, Meth Enzym, 2010) have simulated a 
solvated streptavidin crystal in their seminal papers on crystal-attached 
proteoliposomes. The calibration of the structure factors derived from the 
hydrated streptavidin protein model against the experimental density proved 
necessary for faithful subtraction of the liposome density. Such an internal 
scaling reference represents the gold standard.

As concerns programs, I prefer SFALL and FFT from the ccp4 program collection; 
simply because they have been written, tested and refined over decades by 
countless crystallographers. SFALL uses x-ray scattering factors for each atom 
type. This method can produce adequately sampled density for a full virus shell 
in a large box. Scaling the experimental map to the average amplitudes (per 
shell) of such a synthetic map usually results in better density than simple 
sharpening by negative B-factor.

CNSSOLVE can produce density using the input file MODEL_MAP.
There are options for including bulk solvent and the possibility to use atomic 
scattering factors for electrons rather than x-rays. This should result in the 
best simulated density short of a fully hydrated MD simulation.

EMAN's PDB2MRC appears to use gaussian blobs to simulate atoms in real space.
SITUS' PDB2VOL has some more options in this respect.

Of course it depends on the what you want to do. But I trust the 
crystallographic programs more for producing realistic density. In addition, 
most EM packages result in inconsistencies regarding header information (e.g. 
origin, column start, space group). If not fixed with an additional step 
(imedit.exe, mapman, etc),  the latter results in the density showing up in the 
wrong place with respect to the model when displayed in crystallographic 
modeling software like O or coot.

    Matthias

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
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

-- 
_________________________________________________
Matthias Wolf, PhD - Postdoctoral Research Fellow
Harrison Laboratory
BCMP, Harvard Medical School
Seeley G. Mudd 130
250 Longwood Ave. Boston, MA 02115
Phone: 617-432-1216, email: wolf at crystal.harvard.edu 
<mailto:wolf at crystal.harvard.edu>
http://crystal.harvard.edu <http://crystal.harvard.edu/>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: https://mail.ncmir.ucsd.edu/mailman/private/3dem/attachments/20110728/204911f0/attachment.html