Closed density map

From: RONG hui Rong
Date: 26 August 2011 15:44


Dear all,

Do you know how to generate  some closed density map (mesh) that can wrap ligand without tangling with electron density map of other residues?

Many Thanks!

Hui

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From: <Herman.Schreuder

I would calculate an omit map. Delete your ligand and use the resulting pdb file to calculate a map. Density for your ligand will show up as positive difference density.

Herman 

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From: Dale Tronrud

  I think the number one criterion for choosing a map for a figure should
be "What am I trying to show in this figure?"   If you simply want an electron
density mesh that covers your ligand calculate an Fcalc map.  This type of
figure is usually worthless in a research paper but may have value in a
tutorial setting.

  More common is a figure whose intent is to justify your identification
of the ligand and its conformation.  In that case you want a map that has
as little model bias toward you interpretation as possible.  As Herman noted,
this is often calculated as an omit map with some additional effort to
removed secondary model bias (e.g. refining the model with the ligand omitted).
My preference is to show the very map that convinced me, since that map is
certainly not biased by models that were built later.  You should be the
harshest critic of your own models so that map should have been very convincing
to have convinced even you.

  If the density in that map bleeds a little into the protein density, so
be it.  That is not important.

Dale Tronrud