[phenixbb] Similar 2Fo-Fc maps, very different e/A^3 levels (absolute levels)

[Dale Tronrud]

   I'm not an expert on twining, but I think you should first decide if
your crystal is twinned, then use the map that is calculated based on
that determination.  How the map "looks" is not a very rigorous basis
for making a decision about anything, unless you have no bulk solvent
regions or your helices "look" left-handed.  The fact that your free R
does not drop when you refine assuming twining does not encourage me.

   The electron density values you quote seem low to me as well
(referring to Edward Berry's letter).  The expected rms value of a map
will depend on resolution.  The rms of the map is directly related to
the rms of its Fourier coefficients, so when the coefficients get
weaker the rms of the map will drop.  I'm used to an rms of about
0.36 e/A^3 for a 1.5 A resolution map.  For the rms to drop to
0.08 e/A^3 you would have to be at quite a low resolution, but you
have not informed us of that.

   I suspect that the detwining calculation in Map #1 is not being
correctly normalized.  If so, the map will appear identical to the
correctly normalized map, but only after the contour level has been
adjusted.  Since this sort of error does not affect most peoples'
use of the map this is probably not debugged carefully.  The last
time I checked, Coot's ncs averaged maps have very odd numbers for
their absolute density values.  Again, since a spin of the mouse
wheel will make the map look as expected no one seems to care enough
to figure out the problem.

Dale Tronrud

On 12/03/12 09:09, Sam Stampfer wrote:
> Dear Phenix group,
> 
>  
> 
> I am trying to decide which electron density map to use for rebuilding
> my structure in Coot. Both 2Fo-Fc maps appear quite similar at the 1
> sigma level but the absolute electrons per cubic Angstrom (e/A^3) is
> very different.
> 
>  
> 
> When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot
> calls them absolute levels):
> 
> Map #1 2Fo-Fc: 0.0044 e/A^3
> 
> Map #2 2Fo-Fc: 0.0832 e/A^3
> 
>  
> 
> Map #1 was generated using a twinning operator that is typically
> required for this crystal form. Map #2 was generated without the
> twinning operator and it tends to have slightly better 2Fo-Fc density,
> and there is a bit more density (or noise?) in the Fo-Fc map.
> 
>  
> 
> The structure was refined in Phenix and gave a similar Rfree regardless
> of whether a twinning operator was used.
> 
>  
> 
> What does it mean to have this 20-fold difference in electrons per cubic
> Angstroms for my maps? Which map should I use?
> 
>  
> 
> Thanks for your help!
> 
>  
> 
> -Sam
> 
> 
> PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3
> level.
> 
> 
> 
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