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<div class="moz-cite-prefix">Hi Sam,<br>
<br>
I have a guess that may explain this. Scaling in case of twining
and no twinning is done by two different routines. If I recall
correctly one divides map coefficients by overall scale (no
twinning) and the other (twining) doesn't. Sigma-scaled maps are
not sensitive to this but volume scaled maps would be different by
the factor of that overall scale (that's what you observe I
guess). <br>
<br>
Fixing this is in my todo list (but it's not high up in priority
as it's rather inconvenience than a real problem).<br>
<br>
For now I would just use sigma-scaled maps and rely more on map
shape when interpreting it.<br>
<br>
Pavel<br>
<br>
On 12/3/12 9:09 AM, Sam Stampfer wrote:<br>
</div>
<blockquote
cite="mid:CAF_3vPdC4h3LPyG-+iJa8K8kfeP=JAhB8rzB7X8iZJowj4-74w@mail.gmail.com"
type="cite">
<p class="MsoNormal" style="text-align:left" align="left">Dear
Phenix group,</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">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.</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">When
contoured at 1.00 rmsd
in coot, these are the e/A^3 levels (Coot calls them absolute
levels):</p>
<p class="MsoNormal" style="text-align:left;margin-left:40px"
align="left">Map #1 2Fo-Fc: 0.0044
e/A^3</p>
<p class="MsoNormal" style="text-align:left;margin-left:40px"
align="left">Map #2 2Fo-Fc: 0.0832
e/A^3</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">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.</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">The
structure was refined
in Phenix and gave a similar Rfree regardless of whether a
twinning operator
was used.</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">What
does it mean to have
this 20-fold difference in electrons per cubic Angstroms for my
maps? Which map
should I use?</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">Thanks
for your help!</p>
<p class="MsoNormal" style="text-align:left" align="left"> </p>
<p class="MsoNormal" style="text-align:left" align="left">-Sam</p>
<p class="MsoNormal" style="text-align:left" align="left"><br>
</p>
<p class="MsoNormal" style="text-align:left" align="left">PS: The
Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3
level.<br>
</p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
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