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Hi Jason,<br>
<br>
<blockquote
cite="mid:AANLkTimZarnEYnAQPQnpy20tA-SfgjARMcPEhzYUbc=a@mail.gmail.com"
type="cite">Can anybody go through it for me please, or there are
other handy programs that can make anomalous difference map?<br>
</blockquote>
<br>
phenix.maps (from command line or GUI) is THE tool to do this task.
phenix.refine outputs this map too, as yourself or Nat mentioned
already. If the anomalous difference map doesn't show anything, then
I guess the following are among the possibilities: 1) there is
nothing to show, 2) there is something not right with the data
itself, 3) you feed incorrect data into the program or run the
program incorrectly.<br>
<br>
<blockquote
cite="mid:AANLkTik330u3TnixfUTb1fe_h-hRVvCq9U8egB+vHb=T@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">It depends on the ligand, I guess. If
it's large enough and actually<br>
bound, it should be detectable in the Fo-Fc map - this would
be a good<br>
sanity check to make sure that the anomalous map generation is
working<br>
properly.<br>
</blockquote>
<div> </div>
<div>Unfortunately my ligand is fairly small, about 12 atoms.The
Fo-Fc map won't be that helpful.<br>
</div>
</div>
</blockquote>
<br>
I'm quite puzzled about this... We use Fo-Fc maps to find water
oxygens (one single atoms)! Why one would think that 12 molecule is
too small to see it in Fo-Fc map? Am I missing something?<br>
<br>
If you like, you can send me the data and model files and I will try
myself.<br>
<br>
Pavel.<br>
<br>
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