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Phil Jeffrey wrote:
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Something I have never found to work to my satisfaction has been solvent
flattening after molecular replacement where the model is somewhat
partial (i.e. more than 20% of the new structure is not modeled by the
MR solution). In a case I was trying out for someone else a few months
back I used DM with a variety of automatic and more manually-generated
solvent masks, and this produced no significant gain in the phases to my
eyes. So I am left with the suspicion that I'm not using the best methods.
Does anyone have any advice ? - I've found Coulombe and Cygler's 1997
paper (Acta Cryst D53, 426-433) - but I imagine that there is other
information out there that an hour's Googling has yet to turn up.
Thanks
Phil Jeffrey
Princeton, NJ
Your electron density map is based on phases from the molecular
replacement solution model. In this model the solvent is represented as
a vacuum or, more likely, some bulk solvent model you selected. In
either case the model implicitly uses a flat density for the solvent
region. This "flatness" is reflected in the calculated phases that you
use to generate your density map for averaging. Errors in amplitudes
will introduce noise which solvent flattening will reduce but since maps
are dominated by the phase there may not be that much to improve, in
contrast to solvent flattening on an experimentally phased map. NCS
averaging should do much better but you may not have that option.
Bart
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
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Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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