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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. -- ******************************************************* 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: [log in to unmask] WWW: www.genzentrum.lmu.de *******************************************************