[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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> > phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> > http://phenix-onl
>
>
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