[phenixbb] How to eliminate or decrease negative electron density at ligand position

J J phenix.upitt at gmail.com
Wed Oct 13 12:21:58 PDT 2010

Hello everyone,

I have fine electron density 2Fo-Fc around a small ligand (~20 atoms)
binding to my protein (at 1sigma level, all of the ligand atoms are surround
by electron density, resolution=3 angstrom). However, I also see some
negative electron density Fo-Fc surrounding some of the ligand atoms. My
question is should I care about these negative electron density? If I
should, what should I do in order to decrease or eliminate these negative
electron density? I have tried occupancy refinement. It does help to
decrease the negative density. However, it also makes 2Fo-Fc weaker. Another
method I tried is to use tls refinement only for the ligand. It also helped
to decrease the negative electron density. But since the data resolution is
only 3 angstrom, I do not know if I am even allowed to do tls refinement?
Thank you all in advance.


University of Pittsburgh
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