Will ChimeraX deal with data in Fourier space (MTZ format)?
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
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Regarding missing data, unless completeness is quite low filling in with zeroes should be okay I think. I know phenix fills missing terms with Fcalc from model by default, but I think that would not be advisable in chimera due to reliance on the presence of an atomic model to calculate Fcalc. Of course MTZs from single particle work are generally synthetic (created from a map) in which case there will by definition be no missing data. Cheers, Oli On Thu, Feb 4, 2016 at 9:18 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Oliver Clarke -
Tom Goddard