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.<br><br>How would I go about properly normalizing the detwinning calculation, if that were the problem?<br>
<br>Thanks,<br>-Sam<br><br><div class="gmail_quote">On Mon, Dec 3, 2012 at 1:13 PM, Dale Tronrud <span dir="ltr"><<a href="mailto:det102@uoxray.uoregon.edu" target="_blank">det102@uoxray.uoregon.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
� �I'm not an expert on twining, but I think you should first decide if<br>
your crystal is twinned, then use the map that is calculated based on<br>
that determination. �How the map "looks" is not a very rigorous basis<br>
for making a decision about anything, unless you have no bulk solvent<br>
regions or your helices "look" left-handed. �The fact that your free R<br>
does not drop when you refine assuming twining does not encourage me.<br>
<br>
� �The electron density values you quote seem low to me as well<br>
(referring to Edward Berry's letter). �The expected rms value of a map<br>
will depend on resolution. �The rms of the map is directly related to<br>
the rms of its Fourier coefficients, so when the coefficients get<br>
weaker the rms of the map will drop. �I'm used to an rms of about<br>
0.36 e/A^3 for a 1.5 A resolution map. �For the rms to drop to<br>
0.08 e/A^3 you would have to be at quite a low resolution, but you<br>
have not informed us of that.<br>
<br>
� �I suspect that the detwining calculation in Map #1 is not being<br>
correctly normalized. �If so, the map will appear identical to the<br>
correctly normalized map, but only after the contour level has been<br>
adjusted. �Since this sort of error does not affect most peoples'<br>
use of the map this is probably not debugged carefully. �The last<br>
time I checked, Coot's ncs averaged maps have very odd numbers for<br>
their absolute density values. �Again, since a spin of the mouse<br>
wheel will make the map look as expected no one seems to care enough<br>
to figure out the problem.<br>
<span class="HOEnZb"><font color="#888888"><br>
Dale Tronrud<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On 12/03/12 09:09, Sam Stampfer wrote:<br>
> Dear Phenix group,<br>
><br>
><br>
><br>
> I am trying to decide which electron density map to use for rebuilding<br>
> my structure in Coot. Both 2Fo-Fc maps appear quite similar at the 1<br>
> sigma level but the absolute electrons per cubic Angstrom (e/A^3) is<br>
> very different.<br>
><br>
><br>
><br>
> When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot<br>
> calls them absolute levels):<br>
><br>
> Map #1 2Fo-Fc: 0.0044 e/A^3<br>
><br>
> Map #2 2Fo-Fc: 0.0832 e/A^3<br>
><br>
><br>
><br>
> Map #1 was generated using a twinning operator that is typically<br>
> required for this crystal form. Map #2 was generated without the<br>
> twinning operator and it tends to have slightly better 2Fo-Fc density,<br>
> and there is a bit more density (or noise?) in the Fo-Fc map.<br>
><br>
><br>
><br>
> The structure was refined in Phenix and gave a similar Rfree regardless<br>
> of whether a twinning operator was used.<br>
><br>
><br>
><br>
> What does it mean to have this 20-fold difference in electrons per cubic<br>
> Angstroms for my maps? Which map should I use?<br>
><br>
><br>
><br>
> Thanks for your help!<br>
><br>
><br>
><br>
> -Sam<br>
><br>
><br>
> PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3<br>
> level.<br>
><br>
><br>
><br>
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</div></div></blockquote></div><br>