<div><div>Hi everyone,</div><div><br></div><div>I would like to have commnets
from experts on the following issues.</div><div><br></div><div>I am refining
DNA-protein complex at 3 A resolution and my current Rfree is 21.5 %
(phenix.refine).</div><div><br></div><div>1. </div><div>I am getting
difference map peaks (in Coot) of magnitude less than -5 sigmas (0.24 e/A3)
(~10 or more peaks) and equal number of positive peaks of same
magnitudes.</div><div>The positive peaks hardly have 2fo-fc of more than 1.0
sigma level. I presumed this well could be due to bulk solvent or improper
mask. Therefore I optimized the mask parameters (by giving option under
"General refinement parameters" in phenix.refine GUI). I could get my R free
lower as expected but I still got these peaks back. Although I am not
absolutely sure, but positive peaks are more in polar pocket of protein
and negative peaks are more in non-polar and aromatic pockets. I have PEG, Na
acetate in my crystal soup. What these negative peaks represent
for?</div><div><br></div><div>2. </div><div>During addition of atoms like
Na+, Cl- in map, do one need to careful about of the its coordination valency
in surrounding pocket. ?</div><div><br></div><div>I will be highly thankful to
you for the
same.</div><div><br></div><div>Ravi</div><div><br></div><div><br></div><div><br></div><br>Ravindra D. Makde, PhD<br>Postdoctoral fellow, Tan lab,<br>The Department of Biochemistry and Molecular Biology,<br>The Pennsylvania State University,<br>University Park, PA 16802<br>USA<br><br><br></div>