[phenixbb] Incorrect solvent modelling in Phenix.refine?

David Briggs drdavidcbriggs at gmail.com
Wed Jun 27 01:29:23 PDT 2012

Hi all,

I'm refining a couple of structures of the same protein (well, point
mutants) and I am consistently seeing large (6sig) negative difference
map peaks within some cavities within my protein, present in both the
datasets. As far as I understand, this is because the bulk solvent
scaling parameters are either incorrect, or being incorrectly applied.
I have tried a few things like applying the "Refine solvent mask
(slow)" options, all to no avail.

Resolution is 2.2Å and 2.5Å. Experimental phasing, Xtriage reports no
abnormalities in the data.

Is there anything that I am missing? Do I need to worry about this?



David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
david.c.briggs at manchester.ac.uk
Webs : http://flavors.me/xtaldave
Twitter: @xtaldave
Skype: DocDCB

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