Pavel,
Thanks for pointing that out.
Based on one dataset, it seems to me that using this kind of maps
"no-fill" as an additional guide can help tracing some side-chains.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 8/6/19 12:17, Pavel Afonine wrote:
> For the record, phenix.refine always produces two versions of 2mFo-DFc
> maps, with and without filling in missing Fobs. The one that opens in
> Coot by default is the "filled" map, but you can always load the other
> one for comparisons.
>
> Pavel
>
> On Tue, Aug 6, 2019 at 8:34 AM Ivan Shabalin
> <[log in to unmask] <mailto:[log in to unmask]>>
> wrote:
>
> Dear Clemens,
>
> Thanks!
>
> It sounds like a good test to do on the output .mtz and see if there
> are
> any significant changes in maps after these "filled in" coefficients
> are
> removed.
>
> Ivan
>
> With best regards,
> Ivan Shabalin, Ph.D.
> Research Scientist,
> Department of Molecular Physiology and Biological Physics,
> University of Virginia,
> 1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
> Charlottesville, VA 22908
> https://www.linkedin.com/in/shabalinig/
> https://minorlab.org/person/ivan_s/
>
> On 8/6/19 08:59, Clemens Vonrhein wrote:
> > Dear Ivan,
> >
> > On Mon, Aug 05, 2019 at 05:44:56PM -0400, Ivan Shabalin wrote:
> >> Dear Kay,
> >>
> >> Thanks a lot for your answers!
> >>
> >> To my best understanding, REFMAC does not have an option of for
> restoring
> >> reflections only in certain resolution shells.
> >
> > Remember that you can always do some simple (but powerfull)
> operations
> > within SFTOOLS (*). So using something like
> >
> > read refmac.mtz
> > CALC col resol = 0.5 stol /
> > select col FP = absent
> > absent col FWT if col resol < 3.0
> > absent col PHWT if col resol < 3.0
> > delete col resol
> > select all
> > write refmac_new.mtz
> >
> > might/should do the trick: setting all filled-in FWT/PHWT values to a
> > MNF (missing-number-flag) for reflections with resolution higher than
> > 3A. So you should only have filled-in 2mFo-DFc valeus for the low-res
> > data (3A and lower).
> >
> > But check those commands above (typed from memory)
> >
> > Cheers
> >
> > Clemens
> >
> > (*) there is very little one can't do with SFTOOLS
> >
>
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