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Hi,<br>
<br>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What
Pavel describes is how to get a “difference map”. But it is
not an “omit map” per the original definition.</span></p>
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<br>
perhaps we are getting into terminology here.. I'm sticking to the
original paper by T. Bhat.<br>
<br>
Difference map is F1-F2, F1=w1*Fobs, F2=w2*Fmodel. I believe you can
prefix it with "omit" if you omit something (remove part of model)
from F2.<br>
<br>
<blockquote
cite="mid:AEB7C96227D9D049AB2CBD26D1153C290144451DF20A@USCTMXP51003.merck.com"
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p>The
omitted part should never have been part of the model during
any refinement step before the omit map is calculated. The
purpose is to prevent bias.</span></p>
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<br>
This is where it gets into nuances not discussed in the original
paper, if memory serves.<br>
<br>
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cite="mid:AEB7C96227D9D049AB2CBD26D1153C290144451DF20A@USCTMXP51003.merck.com"
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style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p>If
the model has already been refined with a ligand, then the
technique of simulated annealing refinement can be used to
remove the bias after removing the ligand. This approximates
an “omit map” (still one may argue not a real “omit map”,
but close enough).</span><br>
</p>
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</blockquote>
<br>
Yes, this seems to be the common mindset. But I'm yet to see a
convincing example with clear illustration of such bias. I believe
this<br>
<br>
1) remove ligand;<br>
2) do some refinement (optionally, don't believe really necessary!);<br>
3) compute mFo-DFc map;<br>
<br>
should be good enough in most cases.<br>
<br>
Pavel<br>
<br>
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