[sharp-discuss] Heavy atom density

esserlo at helix.nih.gov esserlo at helix.nih.gov
Mon May 11 16:00:52 CEST 2015


   it's probably been too long that I did a full-fledged experimental phase
determination, which might explain my puzzlement over the following

In my SIRAS case, with a good native but still better Hg derivative data set
to resolutions of about 3.7 and 3.3 A respectively, I do get pretty good
experimental phases with Auto Sharp 2.8.1 SUSHI 3.10.1. So I am happy. However
in density modification and later on in refinement that includes experimental
phases (HL coefficients) I do get petty strong features for the Hg atom sites.
Since there are bulky residues in the vicinity, there is a tendency for them
to move into the strong ghost sites of Hg. Without experimental phase support,
things clear up (no pseudo Hg density, obviously) but I would say that overall
refinement clearly benefits from having experimental phases around.
{Refinements were done in BUSTER and Phenix with pretty much the same effect}

Maybe I am picking up the wrong coefficients ? I did use HLA-D from Sharp
which are the description of the calculated phase probability and my
understanding is that this is the right set to use. I am aware of the
documentation that speaks of phases with average heavy atom contribution like
PHIBshasol but there is also PHIcentshasol which is "light atoms only". I
tried all of them (with and without average heavy atom contribution ) in ccp4
DM: Density modification and averaging clearly have beneficial effects, but I
still see pronounced density stemming from Hg. No matter what I do.

Well, is this to be expected that even the "light atoms only" phase contain
information about the position of Hg atoms?

Any suggestions ?



More information about the sharp-discuss mailing list