The main issue is that carboxyls seem to be invisible and Coot tries to fit
them as though the map had them there
Well, if the atoms are part of the model, then Coot will try to fit them to
the "data." I routinely chop off GLU and ASP side-chain when modelling into
cryo-EM maps (that's what the K key is for).
That seems unnecessarily harsh. Remember that EM maps do not show electron
density but electric potential, so undamaged negatively charged moieties
should occur at negative density levels. There is an "Aha-Erlebnis" paper (at
least, that's the effect it had on me :-) ) by Jimin Wang and Peter Moore
(entitled "On the interpretation of electron microscopic maps of biological
macromolecules") on this very topic in last month's EM-special of Protein
Science, Vol 26, pp 122-129.
--Gerard
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Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
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