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.

Cheers,

Oli

On Thu, Feb 4, 2016 at 12:27 AM, Tom Goddard <goddard@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@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

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