[chimerax-users] Interactive map sharpening and filtering?

[Tom Goddard]

I guess by low-pass filtering you mean that in Fourier space the radial falloff scale factor is exactly 1.0 out to some frequency and then drops off gradually, where as a Gaussian convolution starts dropping from 1.0 gradually right from 0 frequency.  Using different kernels (radial scale factor functions) would be easy — they just need to be defined by parameters that can be passed to the command.  For low pass you probably need a minimum frequency and a maximum frequency giving the range of the rolloff.

We didn’t provide many map filtering options in Chimera 1, mostly you would use other software like EMAN2 to do that.  But I can extend the capabilities in ChimeraX if there is interest.

	Tom


> On May 10, 2017, at 4:29 AM, Aaron Lewis <alewis at mrc-lmb.cam.ac.uk> wrote:
> 
> I'd add that there is an important difference between Gaussian filtering and band-pass filtering: Gaussian filtering blurs (sharpens) everything by a specified amount, whereas low-pass (high-pass) filtering imposes a minimum amount of blurriness (sharpness). This often makes band-pass filtering the right choice for images with heterogenous resolution, because you often want to blur the noisiest, sharpest parts without blurring the smoothest, blurriest parts. Cryo-EM maps often fall in this category, and thus represent a common use case.
> 
> On Wed, May 10, 2017 at 2:54 AM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> This is just like ChimeraX Gaussian filtering which does a convolution with a Gaussian in Fourier space.  That is relatively fast — a few seconds for a 256**3 map.  You can already do sharpening with the “invert” option to the gaussian filtering command (“vol gaussian #1 1.5 invert true”).  Gaussian filtering is one form of low pass filtering — others could be added.  I think it would be nice to allow a very fast (10 updates per second) test filtering on a small region using a mouse drag to figure out the desired parameters.  But I never spent to the time to figure out a user interface (what small region, how do you undo, how do you then apply to full map, …).
> 
>         Tom
> 
> 
> > On May 6, 2017, at 10:27 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
> >
> > Hi,
> >
> > Has any consideration been given to adding the capacity for fourier-space map sharpening/low pass filtering to ChimeraX? I’m not sure whether or not it is feasible speed wise, but if it is it would be a very useful addition for EM, allowing one to easily try different sharpening B-factors/low pass cutoffs and save the resulting map(s).
> >
> > Cheers
> > Oli
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