[Chimera-users] Will ChimeraX deal with data in Fourier space (MTZ format)?

Oliver Clarke olibclarke at gmail.com
Thu Feb 4 00:18:41 PST 2016

Hi Tom,

NCS shouldn't matter for just doing the FFT unless I am missing something.
Not sure re what to do with missing data - perhaps would it be possible for
ChimeraX to plug into the same cctbx framework (
http://cctbx.sourceforge.net/current/python/cctbx.html  ;
https://www.phenix-online.org/cctbx/) that phenix uses for many of these
operations? Alternatively a lot of the same operations are implemented in a
more single-particle focused manner in EMAN2.1.

As I mention, this would not just be useful for x-ray - I mostly work with
single particle cryoEM data and I would find it very very handy -
particularly sharpening, low pass filtering and otherwise modifying maps is
I think more convenient in fourier space.


On Thu, Feb 4, 2016 at 12:27 AM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>   Yes it would be nice for ChimeraX to be able to do the Fourier transform
> and other steps to convert an MTZ structure factors file to a density map.
> Others have requested this but no one has ever pointed me to documentation
> on how missing data and NCS symmetry are handled in this conversion.  I’ve
> looked online but never found good enough info to make it easy for me.  If
> you have detailed info on this I’ll look at it.
>   We are working with Paul Adams at LBNL to make ChimeraX and Phenix talk
> to each other, but our focus will likely be on cryoEM more than x-ray.
>         Tom
> > On Feb 3, 2016, at 9:26 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> >
> > Hi,
> >
> > I was just wondering whether reading MTZ files and calculating maps
> derived from them is on the cards for ChimeraX?
> >
> > This would have obvious advantages for crystallographers using the
> package, but also increasingly for cryoEM folks - I typically convert my EM
> maps to reciprocal space for use in Coot, and this has certain advantages -
> e.g. being able to perform operations in Fourier space (e.g. low pass
> filtering, B-factor sharpening) at the time the map is loaded.
> >
> > Cheers,
> > Oli
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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