[phenixbb] Strange negative density when refining at low resolution

Andrew Purkiss-Trew andrew.purkiss-trew at cancer.org.uk
Fri Feb 20 06:35:23 PST 2009

Dear Phenixers

	I've been helping a colleague with a dataset at ~3.8 Angstroms (phases
and map from AutoSharp using SAD phasing). At the moment he has an
incomplete polyALA model consisting of two chains related by NCS and a
few extra sections. Refinement seems to proceed OK using phenix.refine
version 1.4-3, but the resultant maps have blobs of negative density in
the core of the protein. I am assuming that these are a side-effect of
the bulk-solvent correction part of the refinement which is confusing
the region where the protein sidechains would be as solvent. There are
no corresponding negative peaks on the surface of protein, but some
positive peaks where larger sidechains may be.

	Is this interpretation likely to be correct and if so, which parameter
should be altered in the Bulk Solvent section of the input to allow for
a bigger mask around the protein. I see that it isn't recommended to
change the parameters, but the refinement.mask.solvent_radius=1.0 looks
like an obvious candidate.

	If necessary, I can get an image made showing the maps.


	Andrew Purkiss-Trew

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