Most density modification programs include aspects of solvent flattening
- it is unnecessary and apparently counter-productive to do it again..
Eleanor
On 10/17/2010 08:29 PM, Wu, Mousheng wrote:
Dear All,
I have a MAD dataset at 4Å and shelxD can find clear-cut 10 solutions (my
protein has 12 methionines). I ran autosharp to refine them followed by density
modification. After density modification, I ran solvent flattening. Then I
calculated the anomalous map using the phase from sharp and the electron
density map from solvent flattening. The anomalous map shows the density
around these 10 selenium sites are clear and round. However, the density map
from solvent flattening showed that only 4 selenium sites have clear and round
density. The density around these 4 sites clearly showed beautiful helices.
surprisingly, other 6 selenium sites have poor density or no density at all.
The electron density around them is not very good and the predicted helical
density is flat. I check the electron density before I ran solvent flattening.
The result is same. I am quite confused about the big difference from these
two maps. I also try SnB to find the selenium sites. The solutions
are same as those from ShelxD. But How to explain the poor density around the
selenium sites in the density modification map? Is there any problem with my
selenium sites? Any suggestion from crystallographic experts? Thanks.
Mousheng Wu, PhD
Center for Membrane Biology
Department of Biochemistry and Molecular Biology
The University of Texas Medical School at Houston
6431 Fannin Street, Houston, TX, USA, 77030
