On 09.01.2015 08:56, Armando Albert wrote:
Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction
instead of mask based scaling?
Armando
Dear Armando,
yes: the mask bulk solvent correction depends on the proper calculation
of a protein mask. The bulk solvent density is then assigned outside the
protein mask. This mask calculation is based on one or two radii around
the protein atoms and is always a compromise. Sometimes, the protein
mask misses really empty cavities usually surrounded by hydrophobic
residues, wrongly filling these cavities with bulk solvent density. This
results in relatively large blobs with negative difference density.
Sometimes, the protein mask covers narrow cavities really filled with
bulk solvent electron density, which is then missing in the model. This
results in positive difference densities, that are not easy to
interpret. The Babinet bulk solvent correction only uses two parameters,
is less effective in describing the contribution of the bulk solvent to
the scattering, but is free of these artefacts. I use the Babinet bulk
solvent correction sometimes as a control if I'm not sure about the
origin of possibly important difference density peaks in narrow regions.
Best regards,
Dirk.
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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