Add smoothing option to fitmap command

[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,

Would it be possible to add an option to fitmap (in either/both chimera/chimerax) to restrict the spatial frequencies used for fitting? That is, to fit gaussian filtered versions of the input maps behind the scenes, but apply the resulting transform to the unfiltered maps? Filtering maps to say 15 Å gives a much better radius of convergence in my experience - much less prone to getting stuck in local minima.

...

Cheers
Oli

[Tom Goddard]

I also have seen that using a smoothed map increases the radius of convergence in fitting. So in ChimeraX I will sometimes use

volume gaussian #2 sdev 5
fit #1 in #2

to fit into a smoothed map. I agree it might be convenient to have an option to the fit command so this could be done in one command like "fit #1 in #2 smooth 10". The Gaussian filtering does a Fourier transform to do the smoothing and can be a bit slow (10 seconds for larger maps), and maybe binning would be a faster option achieving the same result, could have "fit #1 in #2 bin 4". With such an option I envision only smoothing the map being fit into. If #1 is a map I don't think smoothing it also will increase the radius of convergence. An issue with these proposed options is whether the smoothed map should be kept (and shown in Volume Viewer) after the fit operation so it can be used again. Not sure what is best there. It is inconvenient to keep it if it will not be used again since it adds needless models. But it can also show you what you actually fit into (how smooth it is), and it can be used again without recomputing if you want to adjust the position of #1 and fit again.