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

Dale Tronrud det102 at uoxray.uoregon.edu
Mon Dec 3 11:33:13 PST 2012

On 12/03/12 10:38, Sam Stampfer wrote:
> Thanks so much for the replies! The structure is being refined at 2.74 A
> resolution, but I may need to raise the cutoff to 2.9 or so. The crystal
> was anisotropic.

I would not be surprised to see that the 1 rms level of a 3 A
resolution map would be at 0.08 e/A^3.  You can't really represent the
"peaky" center of atoms with only low resolution Fourier coefficients.
>
> How would I go about properly normalizing the detwinning calculation, if
> that were the problem?

If your crystal is not twinned then this is not a problem for you.

If there is a normalization problem with the detwining code it is up
to the authors to figure it out.  There is little you can do.  However,
since I don't expect the variation of a detwinned map to  differ
much from the untwinned map it appears that you could just multiply
your detwinned map by 20 to make it roughly the level of your map #2.

Dale Tronrud

>
> Thanks,
> -Sam
>
> On Mon, Dec 3, 2012 at 1:13 PM, Dale Tronrud <det102 at uoxray.uoregon.edu
> <mailto:det102 at uoxray.uoregon.edu>> wrote:
>
>
>        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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>
>

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