Specify resolution in volume gaussian command instead of standard deviation

[olibclarke@…]

Begin forwarded message:

From: Oliver Clarke
Subject: [Chimera-users] Gaussian filter prior to fitmap?
Date: October 1, 2019 at 5:50:12 AM PDT
To: UCSF Chimera Mailing List <chimera-users@…>

Hi,

...

In general I also wish that when applying a gaussian filter in Chimera (or chimerax), the approximate equivalent in spatial frequency terms was indicated - e.g. if I am applying a gaussian filter of sdev x to a map of pixel size y, what lowpass filter does this effectively equate to?

...

Cheers
Oli

[Tom Goddard]

I agree that specifying the standard deviation of the Gaussian in a Gaussian filter is not the best -- it would be better if the number specified directly indicated how much the resolution will be decreased. Would be nice if we had say "volume gaussian #1 blur 10" which would reduce my 5 Angstrom resolution map to 15 Angstroms. Currently you have to say instead something like "volume gaussian #1 sdev 2.25". The factor converting between resolution and Gaussian standard deviations is about 0.225 (= 1 / (pi * sqrt(2)) as used by the molmap command when simulating a map from an atomic model. But it is not has simple as that. The "blur 10" option would not add 10 to the resolution. When you convolve a Gaussian with a Gaussian the result is a Gaussian but its width is not the sum of the widths of the two input Gaussians -- instead it is sqrt(sigma12 + sigma22). So the blur option example would really give effective resolution sqrt(5*5 + 10*10) = 11 Angstroms. Still it be easier to choose the number than the current standard deviation.

[Tristan Croll]

A suggestion: the common approach throughout both the crystallographic and cryo-EM communities is to report/use the sharpening or smoothing B-factor (8*pi2*{variance of applied gaussian}). Would be really great to have that as at least an option since it should be familiar to everyone who's really active in the field.

volume gaussian #1 Bfactor 20 # approximately equivalent to `volume gaussian #1 sDev 0.5`
volume gaussian #1 Bfactor -20 # Sharpening, approx. equivalent to `volume gaussian #1 sDev 0.5 invert true` 

[Tristan Croll]

Argh! Damned auto-formatting. That should of course be B = 8*pi**2*{variance of applied gaussian}.

[Tom Goddard]

I added the volume gaussian bfactor option suggested by Tristan including negative values meaning to sharpen (ie. implies "invert true").