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Hi Alexei,<br>
<br>
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When refining a crystal structure in phenix.refine, presence of
explicit hydrogens usually decreases the number of clashes. </div>
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<br>
that's a desirable outcome. But that depends on many factors and
varies case by case.<br>
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">In the real-space
refinement of a model against a cryo-EM map, however, explicit
hydrogens did not improve the clashscore. Is this normal? </div>
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<br>
May be this is a case where they don't. And they may do in some
other case.<br>
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">Does it depend on
resolution?</div>
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<br>
Generally, yes. At higher resolution the map should have more
impact.<br>
<br>
Pavel<br>
<br>
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