Dear Suparno,
In general, it will be quite challenging to make conclusion from
structure refined against data at 4 A... Maybe cryoEM could help?
I think it is acceptable to present a sharpened map, you just have to
state a B-value which was used in sharpening calculation. You can play
with setting of such B-value. For instance, in Coot, there is a dialog
Calculate -> Map Sharpening/Blurring. At some point, you would see
artifacts in map caused by noise which was amplified to much so set a
B-value wisely.
I do not feel confident to simply answer your question "Is it OK to
solely rely on the FEM?", sorry.
Some people say that Buster does a good job when dealing with low
resolution data. There is also a useful program Lorestr in CCP4. I would
be personally interested if intensity based refinement in Servalcat
would help you, probably in the setup with --jellybody --ncsr , fixed
all B-values to a reasonable value, and with ProSMART restraints based
on reference structures.
Good luck!
Martin
On 27/01/2026 18:06, Suparno Nandi wrote:
Hello all,
I have a 4.0 A crystal structure of an enzyme-ribosome complex, and because of
the poor map quality, I have enhanced the map quality by using the
feature-enhanced map (FEM) for crystal structures and the autosharpen function
available for cryo-EM structures in PHENIX.
I would like to know if I need to show the unsharpened map (the normal 2Fo-Fc
map) along with the sharpened maps for the region of interest? In some
instances, the unsharpened map does not show density for certain residues,
therefore is it OK to solely rely on the FEM? Also, is it correct to use the
autosharpen function that is available for cryo-EM structures but not for xtals?
Best,
Suparno Nandi, Ph.D.
Dept. of Biochemistry
Emory University
Atlanta, GA, USA
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