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Hi,<br>
<br>
<blockquote
cite="mid:566071439.4401615.1480607848697@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">Supposed by
phenix.real_space_refine I got a PDB of protein-ligand, will you
please let me know how to get the subtraction map (difference
map?) which only show the density of the ligand, so that I can
see whether the ligand was well resolved in the map, or whether
the built ligand fits well with the ligand density?</div>
</blockquote>
<br>
it's not yet available (assuming you are asking for this to be done
in real space). However you should be able to use your original
cryo-EM map to infer this information.<br>
<br>
Another alternative (which I can't dislike more) is to convert
cryo-EM map into structure factors, run a round of phenix.refine
refinement, and that will give you an MTZ with 2mFo-DFc and mFo-DFc
map coefficients (which, by construction, will be model biased,
unlike your original cryo-EM map!). How much sense they would make
in this case that I can't tell.<br>
<br>
Pavel<br>
<br>
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